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Releases: Gilead-BioStats/gsm

v1.6.0

05 Apr 17:06
@mattroumaya mattroumaya
v1.6.0
3d1b61d
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v1.6.0

gsm v1.6.0

This release includes significant qualification testing updates, improvements to reporting, updates to default variable names, and updates to mappings and workflows.

Mapping and Workflow Updates

  • All default KRI workflows (except for Screen Failure) only include enrolled patients by default.
  • Mappings have been updated to reflect expected default variable names.
  • A new mapping_domain has been added.

Reporting

  • Small bugs were squashed that resulted in erroneous data being reported about workflow status.

Qualification Testing and Reporting

  • Major refactor for the qualification report, which adds more detail, and more easily-read tables.
  • Qualified functionality for 24 functions that include the bulk of the entire analytics pipeline in {gsm}

What's Changed

Full Changelog: v1.5.0...v1.6.0

Contributors

samussiah, mattroumaya, and 3 other contributors
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v1.5.0

07 Feb 22:16
@mattroumaya mattroumaya
v1.5.0
81a0a37
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v1.5.0

gsm v1.5.0

This release includes changes to Protocol Deviation mapping and analysis, significant qualification testing updates, improvements to reporting, and workflow updates:

Protocol Deviation Mapping and Assessment

  • PD_Map_Raw() has been split into two separate functions: PD_Map_Raw_Binary() and PD_Map_Raw_Rate().
  • PD_Assess() has been split into two separate functions: PD_Assess_Binary() and PD_Assess_Rate().
  • The default Important Protocol Deviation QTL now uses the binary PD mapping and assessment.

Qualification Testing

  • Management of qualification specifications is now done in a .csv file, rather than separate YAML files.
  • Most mapping and assess functions are now qualified.

Reporting

  • New feature added to the output of Study_Report() to highlight an individual site/group in any given visualization.
  • New feature added to the output of Study_Report() to hightlight an individual site/group across all visualizations.

What's Changed

Full Changelog: v1.4.1...v1.5.0

Contributors

samussiah, mattroumaya, and 3 other contributors
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v1.4.1

20 Dec 16:38
@samussiah samussiah
v1.4.1
59b40fe
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v1.4.1

v1.4.1 modifies flagging logic to avoid flagging sites with insufficient data collected.

What's Changed

Full Changelog: v1.4.0...v1.4.1

Contributors

mattroumaya and Zhongkai-Wang
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v1.4.0

19 Dec 15:09
@mattroumaya mattroumaya
v1.4.0
ed83d7c
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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
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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
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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
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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
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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
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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
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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
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