From e3c86cdd89598217bcba4d8c7fba6df74054ca16 Mon Sep 17 00:00:00 2001 From: jreps Date: Wed, 15 Mar 2023 21:05:00 -0400 Subject: [PATCH] updating website for new release --- DESCRIPTION | 2 +- NEWS.md | 5 ++++ docs/404.html | 2 +- docs/articles/InstallationGuide.html | 2 +- .../UsingCharacterizationPackage.html | 24 +++++++++---------- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 6 ++++- docs/pkgdown.yml | 2 +- docs/pull_request_template.html | 2 +- docs/reference/Characterization-package.html | 2 +- .../computeAggregateCovariateAnalyses.html | 2 +- ...computeDechallengeRechallengeAnalyses.html | 2 +- ...puteRechallengeFailCaseSeriesAnalyses.html | 2 +- .../reference/computeTimeToEventAnalyses.html | 2 +- .../createAggregateCovariateSettings.html | 2 +- .../createCharacterizationSettings.html | 2 +- .../createCharacterizationTables.html | 2 +- .../createDechallengeRechallengeSettings.html | 2 +- docs/reference/createSqliteDatabase.html | 2 +- docs/reference/createTimeToEventSettings.html | 2 +- .../exportAggregateCovariateToCsv.html | 2 +- docs/reference/exportDatabaseToCsv.html | 2 +- .../exportDechallengeRechallengeToCsv.html | 2 +- .../exportRechallengeFailCaseSeriesToCsv.html | 2 +- docs/reference/exportTimeToEventToCsv.html | 2 +- docs/reference/index.html | 2 +- .../loadAggregateCovariateAnalyses.html | 2 +- .../loadCharacterizationSettings.html | 2 +- .../loadDechallengeRechallengeAnalyses.html | 2 +- ...loadRechallengeFailCaseSeriesAnalyses.html | 2 +- docs/reference/loadTimeToEventAnalyses.html | 2 +- .../runCharacterizationAnalyses.html | 2 +- .../saveAggregateCovariateAnalyses.html | 2 +- .../saveCharacterizationSettings.html | 2 +- .../saveDechallengeRechallengeAnalyses.html | 2 +- ...saveRechallengeFailCaseSeriesAnalyses.html | 2 +- docs/reference/saveTimeToEventAnalyses.html | 2 +- docs/reference/viewCharacterization.html | 2 +- 40 files changed, 59 insertions(+), 50 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4904867..0ad58a0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: Characterization Type: Package Title: Characterizations of Cohorts -Version: 0.1.0.9000 +Version: 0.1.1 Date: 2023-03-13 Authors@R: c( person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index 79c5acd..0fb8b60 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +Characterization 0.1.1 +====================== + +Fixing bug where cohort_counts were not being saved in the database + Characterization 0.1.0 ====================== diff --git a/docs/404.html b/docs/404.html index 20886a8..ac0bc8f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/articles/InstallationGuide.html b/docs/articles/InstallationGuide.html index a2b2c58..1f631f2 100644 --- a/docs/articles/InstallationGuide.html +++ b/docs/articles/InstallationGuide.html @@ -33,7 +33,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/articles/UsingCharacterizationPackage.html b/docs/articles/UsingCharacterizationPackage.html index c2be504..6557e69 100644 --- a/docs/articles/UsingCharacterizationPackage.html +++ b/docs/articles/UsingCharacterizationPackage.html @@ -33,7 +33,7 @@ Characterization - 0.1.0 + 0.1.1 @@ -165,28 +165,28 @@

Setup | | 0% | |======================================================================| 100% -
## Executing SQL took 0.00634 secs
+
## Executing SQL took 0.00908 secs
## Creating cohort: Diclofenac
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.00962 secs
+
## Executing SQL took 0.00446 secs
## Creating cohort: GiBleed
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.0088 secs
+
## Executing SQL took 0.00896 secs
## Creating cohort: NSAIDs
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.0492 secs
+
## Executing SQL took 0.0542 secs
## Cohorts created in table main.cohort
##   cohortId       name
 ## 1        1  Celecoxib
@@ -4007,8 +4007,8 @@ 
Dechallenge Rechallenge
-
## Executing SQL took 0.00906 secs
-## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.0708 secs
+
## Executing SQL took 0.00792 secs
+## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.0625 secs

If you would like to save the results you can use the function saveDechallengeRechallengeAnalyses and this can then be loaded using loadDechallengeRechallengeAnalyses.

@@ -4114,8 +4114,8 @@

Dechallenge Rechallenge -
## Executing SQL took 0.0936 secs
-## Computing dechallenge failed case series for 3 target IDs and 1 outcome IDs took 0.135 secs
+
## Executing SQL took 0.0925 secs
+## Computing dechallenge failed case series for 3 target IDs and 1 outcome IDs took 0.133 secs

The results are Andromeda objects that can we viewed using dplyr. There is just one table named rechallengeFailCaseSeries:

@@ -4212,7 +4212,7 @@

Time to Event## Connecting using SQLite driver ## Uploading #cohort_settings ## -## Inserting data took 0.00473 secs +## Inserting data took 0.0043 secs ## Computing time to event results 
## 
   |                                                                            
@@ -4249,8 +4249,8 @@ 
Time to Event## Executing SQL took 0.0428 secs
-## Computing time-to-event for T-O pairs took 0.16 secs
+
## Executing SQL took 0.0418 secs
+## Computing time-to-event for T-O pairs took 0.145 secs

If you would like to save the results you can use the function saveTimeToEventAnalyses and this can then be loaded using loadTimeToEventAnalyses.

diff --git a/docs/articles/index.html b/docs/articles/index.html index c31bf3e..e50dfae 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/authors.html b/docs/authors.html index d5c9951..9dfa84f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/index.html b/docs/index.html index a809885..1f63a1c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/news/index.html b/docs/news/index.html index 0cdf562..2dddd1d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 @@ -72,6 +72,10 @@

Changelog

Source: NEWS.md +
+

Characterization 0.1.1

+

Fixing bug where cohort_counts were not being saved in the database

+

Characterization 0.1.0

  • added support to enable target cohorts with multiple cohort entries for the aggregate covariate analysis by restructing to first cohort entry and ensuring the subject has a user specified minPriorObservation days observation in the database at first entry and also perform analysis on first outcomes and any outcome that is recorded during TAR.
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 33dd174..036bdeb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: InstallationGuide: InstallationGuide.html UsingCharacterizationPackage: UsingCharacterizationPackage.html -last_built: 2023-03-15T16:42Z +last_built: 2023-03-16T00:54Z diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html index 8e0be78..9233960 100644 --- a/docs/pull_request_template.html +++ b/docs/pull_request_template.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1
diff --git a/docs/reference/Characterization-package.html b/docs/reference/Characterization-package.html index 0037c39..1d1611e 100644 --- a/docs/reference/Characterization-package.html +++ b/docs/reference/Characterization-package.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/computeAggregateCovariateAnalyses.html b/docs/reference/computeAggregateCovariateAnalyses.html index 8ea4096..085e4f9 100644 --- a/docs/reference/computeAggregateCovariateAnalyses.html +++ b/docs/reference/computeAggregateCovariateAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/computeDechallengeRechallengeAnalyses.html b/docs/reference/computeDechallengeRechallengeAnalyses.html index c74d039..311f42c 100644 --- a/docs/reference/computeDechallengeRechallengeAnalyses.html +++ b/docs/reference/computeDechallengeRechallengeAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html index 60cfc21..35496ff 100644 --- a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html +++ b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/computeTimeToEventAnalyses.html b/docs/reference/computeTimeToEventAnalyses.html index 146b10c..ff0d09d 100644 --- a/docs/reference/computeTimeToEventAnalyses.html +++ b/docs/reference/computeTimeToEventAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createAggregateCovariateSettings.html b/docs/reference/createAggregateCovariateSettings.html index a0b0a36..3765fc4 100644 --- a/docs/reference/createAggregateCovariateSettings.html +++ b/docs/reference/createAggregateCovariateSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createCharacterizationSettings.html b/docs/reference/createCharacterizationSettings.html index 5d758d8..755fbf0 100644 --- a/docs/reference/createCharacterizationSettings.html +++ b/docs/reference/createCharacterizationSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createCharacterizationTables.html b/docs/reference/createCharacterizationTables.html index 7eb013f..e3bef67 100644 --- a/docs/reference/createCharacterizationTables.html +++ b/docs/reference/createCharacterizationTables.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createDechallengeRechallengeSettings.html b/docs/reference/createDechallengeRechallengeSettings.html index 8a9fdec..ea36615 100644 --- a/docs/reference/createDechallengeRechallengeSettings.html +++ b/docs/reference/createDechallengeRechallengeSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createSqliteDatabase.html b/docs/reference/createSqliteDatabase.html index 30b14d0..70750dc 100644 --- a/docs/reference/createSqliteDatabase.html +++ b/docs/reference/createSqliteDatabase.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/createTimeToEventSettings.html b/docs/reference/createTimeToEventSettings.html index 4cb3987..d1a87c1 100644 --- a/docs/reference/createTimeToEventSettings.html +++ b/docs/reference/createTimeToEventSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/exportAggregateCovariateToCsv.html b/docs/reference/exportAggregateCovariateToCsv.html index b8dab95..1e1d94e 100644 --- a/docs/reference/exportAggregateCovariateToCsv.html +++ b/docs/reference/exportAggregateCovariateToCsv.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/exportDatabaseToCsv.html b/docs/reference/exportDatabaseToCsv.html index b6d6dd5..e1b473d 100644 --- a/docs/reference/exportDatabaseToCsv.html +++ b/docs/reference/exportDatabaseToCsv.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/exportDechallengeRechallengeToCsv.html b/docs/reference/exportDechallengeRechallengeToCsv.html index d237188..7411746 100644 --- a/docs/reference/exportDechallengeRechallengeToCsv.html +++ b/docs/reference/exportDechallengeRechallengeToCsv.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html index 8fd1a4d..ea6cd1c 100644 --- a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html +++ b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/exportTimeToEventToCsv.html b/docs/reference/exportTimeToEventToCsv.html index a7bbca2..fcd50ba 100644 --- a/docs/reference/exportTimeToEventToCsv.html +++ b/docs/reference/exportTimeToEventToCsv.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 7cc08c8..9c974ba 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/loadAggregateCovariateAnalyses.html b/docs/reference/loadAggregateCovariateAnalyses.html index c4eabb2..2bd1d85 100644 --- a/docs/reference/loadAggregateCovariateAnalyses.html +++ b/docs/reference/loadAggregateCovariateAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/loadCharacterizationSettings.html b/docs/reference/loadCharacterizationSettings.html index 988d7c7..272c8bb 100644 --- a/docs/reference/loadCharacterizationSettings.html +++ b/docs/reference/loadCharacterizationSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/loadDechallengeRechallengeAnalyses.html b/docs/reference/loadDechallengeRechallengeAnalyses.html index 417352f..404959a 100644 --- a/docs/reference/loadDechallengeRechallengeAnalyses.html +++ b/docs/reference/loadDechallengeRechallengeAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html index 3f6b9a8..cab7d7a 100644 --- a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html +++ b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/loadTimeToEventAnalyses.html b/docs/reference/loadTimeToEventAnalyses.html index af61ae4..f6fbc2f 100644 --- a/docs/reference/loadTimeToEventAnalyses.html +++ b/docs/reference/loadTimeToEventAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/runCharacterizationAnalyses.html b/docs/reference/runCharacterizationAnalyses.html index 416f975..b5a253c 100644 --- a/docs/reference/runCharacterizationAnalyses.html +++ b/docs/reference/runCharacterizationAnalyses.html @@ -18,7 +18,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/saveAggregateCovariateAnalyses.html b/docs/reference/saveAggregateCovariateAnalyses.html index db5c47a..55099f9 100644 --- a/docs/reference/saveAggregateCovariateAnalyses.html +++ b/docs/reference/saveAggregateCovariateAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/saveCharacterizationSettings.html b/docs/reference/saveCharacterizationSettings.html index 34ec74e..da41528 100644 --- a/docs/reference/saveCharacterizationSettings.html +++ b/docs/reference/saveCharacterizationSettings.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/saveDechallengeRechallengeAnalyses.html b/docs/reference/saveDechallengeRechallengeAnalyses.html index 9d465f3..db2a78a 100644 --- a/docs/reference/saveDechallengeRechallengeAnalyses.html +++ b/docs/reference/saveDechallengeRechallengeAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html index de8f8b5..948b610 100644 --- a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html +++ b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/saveTimeToEventAnalyses.html b/docs/reference/saveTimeToEventAnalyses.html index 914af23..9d1c0c8 100644 --- a/docs/reference/saveTimeToEventAnalyses.html +++ b/docs/reference/saveTimeToEventAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1 diff --git a/docs/reference/viewCharacterization.html b/docs/reference/viewCharacterization.html index eb0f2a4..65184e8 100644 --- a/docs/reference/viewCharacterization.html +++ b/docs/reference/viewCharacterization.html @@ -17,7 +17,7 @@ Characterization - 0.1.0 + 0.1.1