gsm v2.2.2

v2.2.2

This patch release moves the duckdb dependency from Imports to Suggests to side step an duckdb/duckdb-r#612 related to deployment of gsm.app to Posit Connect.

What's Changed

• v2.2.2 RC by @samussiah in #2021

Full Changelog: v2.2.1...v2.2.2

2021/merge: Merge pull request #2019 from Gilead-BioStats/simplify-params

Remove glossary.

gsm v2.2.1

Overview

This patch release primarily addresses minor report updates bug fixes. Specifically:

• Reduce size of flags over time table by only displaying the most recent 12 periods
• Return an object of class function from GetStrFunctionIfNamespaced()
• Generalize all Flag_*() functions to a single Flag() function
• Use log4r framework set up in v2.2.0 for stopif()/stopifnot() calls
• Add Subject Disposition field to Study Completion

What's Changed

• update readme report links and dev version by @lauramaxwell in #1995
• Fix #1992- always return function in namespace util by @lauramaxwell in #1998
• Closes #1976 wrap all our stop-esque calls into the log4r setup by @zdz2101 in #1994
• add subject disposition by @samussiah in #2004
• Fix 1946 by @samussiah in #1999
• Refactor Flag functions by @jwildfire in #1920
• Add docs and tests for lConfig by @lauramaxwell in #2005
• gsm v2.2.1 release candidate by @lauramaxwell in #2008
• gsm v2.2.1 release by @lauramaxwell in #2009

Full Changelog: v2.2.0...v2.2.1

gsm v2.2.0

Overview

This minor release prepares the gsm to be used as part of a more sophisticated pipeline, through the addition of
flexible logging and hooks for data access. Specifically:

• Use DuckDB for sql queries and data type coercion within RunQuery()
• Implement more flexible logging with the log4r package
• Add the ability to use lConfig and specify load and save hooks for use with local or remote data.
• Allow RunWorkflows to execute code from other packages with GetStrFunctionIfNamespaced().
• Additional minor updates:
  • fix bug that prevented threshold annotations from appearing in Widget_BarChart()
  • remove required from yaml specs
  • update vignettes to align with new yaml specs

What's Changed

• updated class structure by @andersonjake1988 in #1913
• Keep bg color for switch. by @jonthegeek in #1917
• Fix country metadata by @samussiah in #1926
• Fix Ingest return value by @jonthegeek in #1923
• Add Nickname to report header and fix RunQuery bug by @lauramaxwell in #1915
• Update Metrics.yaml to not generate lWorkflows within steps by @lauramaxwell in #1930
• Closes #1928 swaps out last remnants of kable and kableExtra in favor of gt by @zdz2101 in #1932
• Closes #1880 add site/participant target numbers and labels to STUDY.yaml by @zdz2101 in #1899
• Add act_fpfv and est_fpfv to STUDY.yaml spec by @lauramaxwell in #1941
• Closes #1882 adds a toggle to display past year or full data by @zdz2101 in #1931
• PD > IPD and display site activation / participant enrollment in study info. by @samussiah in #1945
• gsm v2.1.2 release candidate by @lauramaxwell in #1942
• Fix table placement in qual report pdf by @lauramaxwell in #1949
• Fix 1801 by @annezheng2 in #1943
• Closes #1937 Display only results of metrics where data is available in reports by @zdz2101 in #1953
• Update query for treatment discontinuation KRIs by @lauramaxwell in #1960
• Remove required from yamls and associated functions by @lauramaxwell in #1951
• add fields to STUDY.yaml by @lauramaxwell in #1957
• Add hooks to RunWorkflow. by @samussiah in #1961
• Fix typo in STUDY.yaml by @jonthegeek in #1969
• Update vignettes by @lauramaxwell in #1970
• Add thresholds back into barcharts by @lauramaxwell in #1975
• Closes #1933 introduces logging capabilities to gsm by @zdz2101 in #1939
• Closes #1964 update RunQuery to apply data types where applicable by @lauramaxwell in #1965
• fix ldata passthrough, resolves #1981 by @dpastoor in #1982
• fix issue in RunQuery related to incomplete column spec by @samussiah in #1986
• add namespacing capability by @dpastoor in #1988
• V2.2.0 rc by @lauramaxwell in #1985
• run styler on 2.2 by @lauramaxwell in #1991

New Contributors

• @annezheng2 made their first contribution in #1943

Full Changelog: v2.1.1...v2.2.0

1990/merge: Merge pull request #1985 from Gilead-BioStats/v2.2.0-rc

V2.2.0 rc

1985/merge: Merge pull request #1982 from Gilead-BioStats/fix-1981

fix ldata passthrough, resolves #1981

v2.1.2

Overview

This patch release primarily addresses minor report updates and handling classes in sql queries properly. Specifically:

• Add method param to RunQuery so that we can use "name__class" method
• update Flags Over Time widget to only show past 12 months by default, but add toggle to show full history
• display site/participant target as n/N (x%) in reports
• display study nickname on report (if present)
• use gt for tables throughout entire package

What's Changed

• updated class structure by @andersonjake1988 in #1913
• Keep bg color for switch. by @jonthegeek in #1917
• Fix country metadata by @samussiah in #1926
• Fix Ingest return value by @jonthegeek in #1923
• Add Nickname to report header and fix RunQuery bug by @lauramaxwell in #1915
• Update Metrics.yaml to not generate lWorkflows within steps by @lauramaxwell in #1930
• Closes #1928 swaps out last remnants of kable and kableExtra in favor of gt by @zdz2101 in #1932
• Closes #1880 add site/participant target numbers and labels to STUDY.yaml by @zdz2101 in #1899
• Add act_fpfv and est_fpfv to STUDY.yaml spec by @lauramaxwell in #1941
• Closes #1882 adds a toggle to display past year or full data by @zdz2101 in #1931
• PD > IPD and display site activation / participant enrollment in study info. by @samussiah in #1945
• gsm v2.1.2 release candidate by @lauramaxwell in #1942

Full Changelog: v2.1.1...v2.1.2

gsm v2.1.1

This patch release addresses the following bugs and style improvements:

• The checkSpec function properly checks Date columns
• Country test data was incomplete, and not based on updates made in v2.1.0
• Move metric table in KRI report to the tabbed viewer for each KRI
• Add appropriate spacing between KRIs in KRI report output
• pkgdown menu subtitle improvement for readability.
• Reporting handles empty tables/dfs appropriately
• Update table styling in reports
• Fix overview text to properly reflect the report, based on GroupLevel

What's Changed

• Closes #1872 fix miscellaneous aesthetics things and issues by @zdz2101 in #1875
• Fix country report by @samussiah in #1876
• Closes #1659 and #1660 to use gt() instead of kbl() in our functions and reports by @zdz2101 in #1884
• Resolve errors related to missing data and an incomplete set of MetricID in dfBounds. by @samussiah in #1889
• Closes #1894 address bug in Input_Rate() for 0 row dataframe inputs for dfNumerator/dfDenominator by @zdz2101 in #1897
• Flag colors by @jonthegeek in #1898
• Make Report_StudyInfo() Friendlier to Shiny by @jonthegeek in #1885
• Closes #1890 and #1900 to properly check for dates and fix other bugs in checkSpec by @lauramaxwell in #1901
• Fix overall group select bug. by @samussiah in #1903
• Closes #1877 and #1883 addressing bugfixes related to StudyID on Report_Setup() and reportingXXXX datasets by @zdz2101 in #1892
• Embed necessary dependencies in Report_StudyInfo(). by @jonthegeek in #1906
• Update rbm-viz. by @jonthegeek in #1907
• Fix country overview text by @lauramaxwell in #1908
• Gsm v2.1.1 release candidate by @lauramaxwell in #1904
• avoid column name conflicts between Groups and Results by @samussiah in #1910
• Release v2.1.1 by @lauramaxwell in #1909

Full Changelog: v2.1.0...v2.1.1

gsm v2.1.0

Overview

This minor release addresses workflow updates which are required for improved modularity and automation. These updates include:

• Specification of all required data sources in all yaml workflow files, via the spec section of the yaml, which are checked
• Allow a master spec document to be constructed via the CombineSpecs.
• Enforce that by default, each yaml file produces only one output- the final output in the workflow steps.
• Parse out the mapping yamls into individual workflows, one per mapped dataframe.
• Create a standard structure for yamls and the directories that yamls are stored in, specified in vignette('gsmExtensions'),

What's Changed

• Prototype Data Specification Framework by @jwildfire in #1746
• Use required param from spec in CheckSpec() by @lauramaxwell in #1786
• Add explicit snapshot date subset to Widget_GroupOverview. by @samussiah in #1789
• Mapping workflow refactor by @jwildfire in #1785
• Add a function to cleanly convert Params to Labels. by @jonthegeek in #1791
• Report_StudyInfo: Show/Hide by @jonthegeek in #1803
• Reporting Workflow Refactor by @jwildfire in #1783
• Add type field and query columns to all specs by @lauramaxwell in #1808
• Add type validation to CheckSpec() by @lauramaxwell in #1814
• Closes #1760 Updating dropdown menu for articles in website by @zdz2101 in #1811
• Closes #1779 Enhance CombineSpecs() with deduplication, enforcing required and adding checks for type by @zdz2101 in #1815
• Closes #1722 Study Status Table display bugfix of indiscriminant first five attributes by @zdz2101 in #1812
• Update PR template by @lauramaxwell in #1826
• Simpler depends by @jonthegeek in #1809
• Update sample reporting data by @lauramaxwell in #1828
• Add all required spec tables to workflows by @lauramaxwell in #1827
• Closes #1795 add assertions/stopifnot for widget inputs by @zdz2101 in #1829
• Closes #1728 Adds footnote to scatterplot widget by @zdz2101 in #1831
• Add subjid to EDC domains in mapping workflow. by @samussiah in #1844
• MakeMetricTable() by @jonthegeek in #1843
• make analysis workflow work by @samussiah in #1847
• MakeStudyInfo() function by @jonthegeek in #1849
• Update checkSpec() cli message to handle _all required by @lauramaxwell in #1851
• Ingest modular by @jwildfire in #1852
• Closes #1636 allows Visualize_Metric() to run on just results by @zdz2101 in #1833
• Refactor Data Ingestion Workflow by @jwildfire in #1841
• Closes #1653 adds Flag Over Time Widget to Study Overview as a tab by @zdz2101 in #1850
• Load/Save - Take 2 by @jwildfire in #1864
• gsm extensions vignette by @lauramaxwell in #1813
• Closes #1859 checks and updates qualification tests in test/testqualification to align with new workflows for v2.1.0 release by @zdz2101 in #1862
• Add rbm-viz v2.1.0. by @samussiah in #1856
• Closes #1863 address small bugs in MakeWorkflowList() run as intended by @zdz2101 in #1869
• Gsm v2.1.0 Release Candidate by @lauramaxwell in #1867

New Contributors

• @zdz2101 made their first contribution in #1811

Full Changelog: v1.9.2...v2.1.0

v2.0.1

Overview

This minor patch release addresses two reporting bugs. The first ensures the summary table is properly filtered and appears in the report html output under each chart widget. The second allows more flexibility to the report output path and file names, and ensure that intermediary rendering occurs in a temporary directory.

What's Changed

• Don't ever use Sys.Date() as SnapshotDate. by @jonthegeek in #1766
• fixes #1757 - renders if package is read-only by @dpastoor in #1768
• Fix summary tables in reports and add metricTable to Visualize_Metric() output by @lauramaxwell in #1769
• update analyticsInput to match with analyticsSummary by @lauramaxwell in #1775
• Release v2.0.1 by @lauramaxwell in #1772

Full Changelog: v1.9.2...v2.0.1