From 2042123ae97da248b5cfa06f3c4a62544e4dac58 Mon Sep 17 00:00:00 2001 From: jreps Date: Wed, 15 Mar 2023 12:48:09 -0400 Subject: [PATCH] preparing new release - updating news - updating website - updating description --- DESCRIPTION | 4 +- NEWS.md | 7 + _pkgdown.yml | 6 +- docs/404.html | 4 +- docs/articles/InstallationGuide.html | 13 +- .../UsingCharacterizationPackage.html | 2429 ++++++++++++++--- docs/articles/index.html | 4 +- docs/authors.html | 8 +- docs/index.html | 25 +- docs/news/index.html | 9 +- docs/pkgdown.yml | 4 +- docs/pull_request_template.html | 4 +- docs/reference/Characterization-package.html | 7 +- .../computeAggregateCovariateAnalyses.html | 4 +- ...computeDechallengeRechallengeAnalyses.html | 4 +- ...puteRechallengeFailCaseSeriesAnalyses.html | 4 +- .../reference/computeTimeToEventAnalyses.html | 4 +- .../createAggregateCovariateSettings.html | 9 +- .../createCharacterizationSettings.html | 4 +- .../createCharacterizationTables.html | 4 +- .../createDechallengeRechallengeSettings.html | 4 +- docs/reference/createSqliteDatabase.html | 4 +- docs/reference/createTimeToEventSettings.html | 4 +- .../exportAggregateCovariateToCsv.html | 4 +- docs/reference/exportDatabaseToCsv.html | 4 +- .../exportDechallengeRechallengeToCsv.html | 4 +- .../exportRechallengeFailCaseSeriesToCsv.html | 4 +- docs/reference/exportTimeToEventToCsv.html | 4 +- docs/reference/index.html | 12 +- .../loadAggregateCovariateAnalyses.html | 10 +- .../loadCharacterizationSettings.html | 8 +- .../loadDechallengeRechallengeAnalyses.html | 10 +- ...loadRechallengeFailCaseSeriesAnalyses.html | 10 +- docs/reference/loadTimeToEventAnalyses.html | 10 +- .../runCharacterizationAnalyses.html | 4 +- .../saveAggregateCovariateAnalyses.html | 10 +- .../saveCharacterizationSettings.html | 8 +- .../saveDechallengeRechallengeAnalyses.html | 10 +- ...saveRechallengeFailCaseSeriesAnalyses.html | 10 +- docs/reference/saveTimeToEventAnalyses.html | 10 +- docs/reference/viewCharacterization.html | 128 + docs/sitemap.xml | 3 + 42 files changed, 2339 insertions(+), 493 deletions(-) create mode 100644 docs/reference/viewCharacterization.html diff --git a/DESCRIPTION b/DESCRIPTION index 40270bb..59aa8d5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Characterization Type: Package Title: Characterizations of Cohorts -Version: 0.0.6 -Date: 2023-02-13 +Version: 0.1.0 +Date: 2023-03-13 Authors@R: c( person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")), person("Patrick", "Ryan", , "ryan@ohdsi.org", role = c("aut")) diff --git a/NEWS.md b/NEWS.md index dc98ade..79c5acd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +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. +- added shiny app + + Characterization 0.0.1 ====================== diff --git a/_pkgdown.yml b/_pkgdown.yml index 89c427c..0549e21 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -87,6 +87,10 @@ reference: - createSqliteDatabase - createCharacterizationTables - exportDatabaseToCsv - + - title: "Shiny App" + desc: > + Functions to interactively exlore the results from runCharacterizationAnalyses(). + contents: + - viewCharacterization diff --git a/docs/404.html b/docs/404.html index 60042e4..20886a8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -115,7 +115,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/InstallationGuide.html b/docs/articles/InstallationGuide.html index fc35bfb..a2b2c58 100644 --- a/docs/articles/InstallationGuide.html +++ b/docs/articles/InstallationGuide.html @@ -33,7 +33,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -96,7 +96,7 @@

Characterization Installation Guide

Jenna Reps

-

2022-12-16

+

2023-03-15

Source: vignettes/InstallationGuide.Rmd @@ -107,7 +107,7 @@

2022-12-16

Introduction @@ -163,7 +163,6 @@

Installing Characterization u

To install using remotes run:

 install.packages("remotes")
-remotes::install_github("OHDSI/FeatureExtraction")
 remotes::install_github("OHDSI/Characterization")

When installing make sure to close any other Rstudio sessions that are using Characterization or any dependency. Keeping @@ -199,7 +198,7 @@

Acknowledgments## ## To cite package 'Characterization' in publications use: ## -## Reps J, Ryan P (2022). _Characterization: Characterizations of +## Reps J, Ryan P (2023). _Characterization: Characterizations of ## Cohorts_. https://ohdsi.github.io/Characterization, ## https://github.com/OHDSI/Characterization. ## @@ -208,7 +207,7 @@

Acknowledgments## @Manual{, ## title = {Characterization: Characterizations of Cohorts}, ## author = {Jenna Reps and Patrick Ryan}, -## year = {2022}, +## year = {2023}, ## note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization}, ## }

@@ -231,7 +230,7 @@

Acknowledgments

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/articles/UsingCharacterizationPackage.html b/docs/articles/UsingCharacterizationPackage.html index 66e5172..c2be504 100644 --- a/docs/articles/UsingCharacterizationPackage.html +++ b/docs/articles/UsingCharacterizationPackage.html @@ -33,7 +33,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -97,7 +97,7 @@

Using Characterization Package

Jenna Reps

-

2022-12-16

+

2023-03-15

Source: vignettes/UsingCharacterizationPackage.Rmd @@ -108,7 +108,7 @@

2022-12-16

Introduction @@ -165,28 +165,28 @@

Setup | | 0% | |======================================================================| 100% -
## Executing SQL took 0.00556 secs
+
## Executing SQL took 0.00634 secs
## Creating cohort: Diclofenac
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.00483 secs
+
## Executing SQL took 0.00962 secs
## Creating cohort: GiBleed
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.0104 secs
+
## Executing SQL took 0.0088 secs
## Creating cohort: NSAIDs
 ## 
   |                                                                            
   |                                                                      |   0%
   |                                                                            
   |======================================================================| 100%
-
## Executing SQL took 0.0512 secs
+
## Executing SQL took 0.0492 secs
## Cohorts created in table main.cohort
##   cohortId       name
 ## 1        1  Celecoxib
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@@ -1127,40 +2791,40 @@ 
Aggreagate Covariates
 

@@ -1171,40 +2835,40 @@ 
Aggreagate Covariates
 

@@ -1215,40 +2879,40 @@ 
Aggreagate Covariates
 

@@ -1259,40 +2923,40 @@ 
Aggreagate Covariates
 

@@ -1303,40 +2967,40 @@ 
Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

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Aggreagate Covariates
 

+      
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 36
@@ -1523,28 +3187,28 @@ 
Aggreagate Covariates
 

-200033
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@@ -1556,7 +3220,7 @@ 
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@@ -1611,31 +3275,31 @@ 
Aggreagate Covariates
 

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 46
 
 
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 36
@@ -1655,25 +3319,25 @@ 
Aggreagate Covariates
 

-400031
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 46
 
 
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 39
@@ -1688,7 +3352,7 @@ 
Aggreagate Covariates
 

-44
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@@ -1732,7 +3396,7 @@ 
Aggreagate Covariates
 

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 36
@@ -1776,7 +3440,7 @@ 
Aggreagate Covariates
 

-44
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-200032
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 31
 
 
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 34
@@ -1831,25 +3495,25 @@ 
Aggreagate Covariates
 

-200000
+20
 
 
 1002
 
 
-850
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 31
 
 
-46
+47
 
 
-38.5658824
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-3.2816028
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 39
@@ -1875,13 +3539,13 @@ 
Aggreagate Covariates
 

-100032
+13
 
 
 1002
 
 
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 31
@@ -1890,10 +3554,10 @@ 
Aggreagate Covariates
 

-38.6165212
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-3.3301766
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 39
@@ -1919,13 +3583,13 @@ 
Aggreagate Covariates
 

-100000
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 1002
 
 
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 31
@@ -1934,10 +3598,10 @@ 
Aggreagate Covariates
 

-38.6469631
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-3.3192555
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 39
@@ -1963,13 +3627,13 @@ 
Aggreagate Covariates
 

-400032
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 1002
 
 
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 31
@@ -1978,10 +3642,10 @@ 
Aggreagate Covariates
 

-38.5828442
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-3.3071156
+3.3112779
 
 
 39
@@ -2007,7 +3671,7 @@ 
Aggreagate Covariates
 

-400000
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 1002
@@ -2343,8 +4007,8 @@ 
Dechallenge Rechallenge
-
## Executing SQL took 0.066 secs
-## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.131 secs

+
## Executing SQL took 0.00906 secs
+## Computing dechallenge rechallenge for 3 target ids and 1outcome ids took 0.0708 secs

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

@@ -2450,8 +4114,8 @@ 
Dechallenge Rechallenge
-
## Executing SQL took 0.104 secs
-## Computing dechallenge failed case series for 3 target ids and 1outcome ids took 0.158 secs

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

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

@@ -2548,6 +4212,7 @@ 
Time to Event## Connecting using SQLite driver
 ## Uploading #cohort_settings
 ## 
+## Inserting data took 0.00473 secs
 ## Computing time to event results
 
## 
   |                                                                            
@@ -2584,8 +4249,8 @@ 
Time to Event## Executing SQL took 0.0434 secs
-## Computing time-to-event for T-O pairs took 0.158 secs

+
## Executing SQL took 0.0428 secs
+## Computing time-to-event for T-O pairs took 0.16 secs

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

@@ -2989,7 +4654,7 @@ 
Run Multiple
 connectionDetailsT <- DatabaseConnector::createConnectionDetails(
   dbms = 'sqlite',
-  server = file.path(tempdir(),'example','sqliteCharacterization', 'sqlite')
+  server = file.path(tempdir(),'example','sqliteCharacterization', 'sqlite.sqlite')
 )
 
 exportDatabaseToCsv(
@@ -3020,7 +4685,7 @@ 
Run Multiple
   

-
Site built with pkgdown 2.0.6.

+
Site built with pkgdown 2.0.7.

 
 
       
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 819227e..c31bf3e 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -89,7 +89,7 @@ 
All vignettes

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/authors.html b/docs/authors.html
index c1598ff..d5c9951 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -90,14 +90,14 @@ 
Citation

     
 
 
-    
Reps J, Ryan P (2022).
+    
Reps J, Ryan P (2023).
 Characterization: Characterizations of Cohorts.
 https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization. 
 

     
@Manual{,
   title = {Characterization: Characterizations of Cohorts},
   author = {Jenna Reps and Patrick Ryan},
-  year = {2022},
+  year = {2023},
   note = {https://ohdsi.github.io/Characterization, https://github.com/OHDSI/Characterization},
 }

 
@@ -112,7 +112,7 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/index.html b/docs/index.html
index 27cfafc..a809885 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -96,6 +96,8 @@
 

 
Characterization
 

+
Build Status codecov.io

+
Characterization is part of HADES.

 

 

 
Introduction
@@ -224,9 +226,28 @@ 
User Documentationpackage website.

 

 

+
Support
+

+
+

+

 
Contributing
 

 
Read here how you can contribute to this package.

+

+

+
License
+

+
Characterization is licensed under Apache License 2.0

+

+

+
Development
+

+
Characterization is being developed in R Studio.

 

 
   
@@ -277,7 +298,7 @@ 
Developers

 
 

   

-
Site built with pkgdown 2.0.6.

+
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/news/index.html b/docs/news/index.html
index 192b085..0cdf562 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -72,6 +72,11 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+
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.
    • 
+
  • added shiny app
    • 
+

     

 
Characterization 0.0.1

 
Initial version

@@ -90,7 +95,7 @@ 
Characte
 

 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index c92d37c..33dd174 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
 pandoc: 2.19.2
-pkgdown: 2.0.6
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   InstallationGuide: InstallationGuide.html
   UsingCharacterizationPackage: UsingCharacterizationPackage.html
-last_built: 2022-12-16T22:10Z
+last_built: 2023-03-15T16:42Z
 
diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html
index a2c7f35..8e0be78 100644
--- a/docs/pull_request_template.html
+++ b/docs/pull_request_template.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -94,7 +94,7 @@ 
NA

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/Characterization-package.html b/docs/reference/Characterization-package.html
index a8f7548..0037c39 100644
--- a/docs/reference/Characterization-package.html
+++ b/docs/reference/Characterization-package.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -88,7 +88,8 @@ 
See also

     

     
Author

     
Maintainer: Jenna Reps reps@ohdsi.org

-    

+
Authors:

 
   
   
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/computeAggregateCovariateAnalyses.html b/docs/reference/computeAggregateCovariateAnalyses.html
index b2e535b..8ea4096 100644
--- a/docs/reference/computeAggregateCovariateAnalyses.html
+++ b/docs/reference/computeAggregateCovariateAnalyses.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -165,7 +165,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/computeDechallengeRechallengeAnalyses.html b/docs/reference/computeDechallengeRechallengeAnalyses.html
index d82e5d0..c74d039 100644
--- a/docs/reference/computeDechallengeRechallengeAnalyses.html
+++ b/docs/reference/computeDechallengeRechallengeAnalyses.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -150,7 +150,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
index 6717c60..60cfc21 100644
--- a/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
+++ b/docs/reference/computeRechallengeFailCaseSeriesAnalyses.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -155,7 +155,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/computeTimeToEventAnalyses.html b/docs/reference/computeTimeToEventAnalyses.html
index 88bfbf0..146b10c 100644
--- a/docs/reference/computeTimeToEventAnalyses.html
+++ b/docs/reference/computeTimeToEventAnalyses.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -155,7 +155,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createAggregateCovariateSettings.html b/docs/reference/createAggregateCovariateSettings.html
index da2ee60..a0b0a36 100644
--- a/docs/reference/createAggregateCovariateSettings.html
+++ b/docs/reference/createAggregateCovariateSettings.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -81,6 +81,7 @@ 
Create aggregate covariate study settings

     
createAggregateCovariateSettings(
   targetIds,
   outcomeIds,
+  minPriorObservation = 0,
   riskWindowStart = 1,
   startAnchor = "cohort start",
   riskWindowEnd = 365,
@@ -99,6 +100,10 @@ 
Arguments

 
A list of cohortIds for the outcome cohorts

 
 
+
minPriorObservation

+
The minimum time in the database a patient in the target cohorts must be observed prior to index

+
+
 
riskWindowStart

 
The start of the risk window (in days) relative to the `startAnchor`.

 
@@ -140,7 +145,7 @@ 
Value

 

 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createCharacterizationSettings.html b/docs/reference/createCharacterizationSettings.html
index 1c5101e..5d758d8 100644
--- a/docs/reference/createCharacterizationSettings.html
+++ b/docs/reference/createCharacterizationSettings.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -122,7 +122,7 @@ 
Details

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createCharacterizationTables.html b/docs/reference/createCharacterizationTables.html
index e708f68..7eb013f 100644
--- a/docs/reference/createCharacterizationTables.html
+++ b/docs/reference/createCharacterizationTables.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -144,7 +144,7 @@ 
Details

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createDechallengeRechallengeSettings.html b/docs/reference/createDechallengeRechallengeSettings.html
index f6d1217..8a9fdec 100644
--- a/docs/reference/createDechallengeRechallengeSettings.html
+++ b/docs/reference/createDechallengeRechallengeSettings.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -123,7 +123,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createSqliteDatabase.html b/docs/reference/createSqliteDatabase.html
index 68017dd..30b14d0 100644
--- a/docs/reference/createSqliteDatabase.html
+++ b/docs/reference/createSqliteDatabase.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Details

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/createTimeToEventSettings.html b/docs/reference/createTimeToEventSettings.html
index 940d4f6..4cb3987 100644
--- a/docs/reference/createTimeToEventSettings.html
+++ b/docs/reference/createTimeToEventSettings.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/exportAggregateCovariateToCsv.html b/docs/reference/exportAggregateCovariateToCsv.html
index 326a99f..b8dab95 100644
--- a/docs/reference/exportAggregateCovariateToCsv.html
+++ b/docs/reference/exportAggregateCovariateToCsv.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/exportDatabaseToCsv.html b/docs/reference/exportDatabaseToCsv.html
index f194dab..b6d6dd5 100644
--- a/docs/reference/exportDatabaseToCsv.html
+++ b/docs/reference/exportDatabaseToCsv.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -144,7 +144,7 @@ 
Details

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/exportDechallengeRechallengeToCsv.html b/docs/reference/exportDechallengeRechallengeToCsv.html
index 0e4988c..d237188 100644
--- a/docs/reference/exportDechallengeRechallengeToCsv.html
+++ b/docs/reference/exportDechallengeRechallengeToCsv.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
index d8a6ecd..8fd1a4d 100644
--- a/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
+++ b/docs/reference/exportRechallengeFailCaseSeriesToCsv.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/exportTimeToEventToCsv.html b/docs/reference/exportTimeToEventToCsv.html
index 30b9e67..a7bbca2 100644
--- a/docs/reference/exportTimeToEventToCsv.html
+++ b/docs/reference/exportTimeToEventToCsv.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -110,7 +110,7 @@ 
Value

 
 
 

-  
Site built with pkgdown 2.0.6.

+  
Site built with pkgdown 2.0.7.

 

 
       
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b59be76..7cc08c8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       
       
         Characterization
-        0.0.4
+        0.1.0
       
     
 
@@ -199,6 +199,14 @@ 
Insert into Database exportDatabaseToCsv() 

         

         
Exports all tables in the result database to csv files

+          
Shiny App 

+          
Functions to interactively exlore the results from runCharacterizationAnalyses().

+        

+          
viewCharacterization() 

+        
viewCharacterization - Interactively view the characterization results

diff --git a/docs/reference/loadAggregateCovariateAnalyses.html b/docs/reference/loadAggregateCovariateAnalyses.html index 3db8869..c4eabb2 100644 --- a/docs/reference/loadAggregateCovariateAnalyses.html +++ b/docs/reference/loadAggregateCovariateAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,13 +78,13 @@

Load the AggregateCovariate results

- 
loadAggregateCovariateAnalyses(saveDirectory)
+ 
loadAggregateCovariateAnalyses(fileName)

Arguments

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -106,7 +106,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/loadCharacterizationSettings.html b/docs/reference/loadCharacterizationSettings.html index b1830e9..988d7c7 100644 --- a/docs/reference/loadCharacterizationSettings.html +++ b/docs/reference/loadCharacterizationSettings.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,12 +78,12 @@

Load the characterization settings previously saved as a json file

- 
loadCharacterizationSettings(saveDirectory)
+ 
loadCharacterizationSettings(fileName)

Arguments

-
saveDirectory
+
fileName

The location of the the json settings

@@ -110,7 +110,7 @@

Details

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/loadDechallengeRechallengeAnalyses.html b/docs/reference/loadDechallengeRechallengeAnalyses.html index c2bb526..417352f 100644 --- a/docs/reference/loadDechallengeRechallengeAnalyses.html +++ b/docs/reference/loadDechallengeRechallengeAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,13 +78,13 @@

Load the DechallengeRechallenge results

- 
loadDechallengeRechallengeAnalyses(saveDirectory)
+ 
loadDechallengeRechallengeAnalyses(fileName)

Arguments

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -106,7 +106,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html index 4a7801f..3f6b9a8 100644 --- a/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html +++ b/docs/reference/loadRechallengeFailCaseSeriesAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,13 +78,13 @@

Load the RechallengeFailCaseSeries results

- 
loadRechallengeFailCaseSeriesAnalyses(saveDirectory)
+ 
loadRechallengeFailCaseSeriesAnalyses(fileName)

Arguments

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -106,7 +106,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/loadTimeToEventAnalyses.html b/docs/reference/loadTimeToEventAnalyses.html index 3563050..af61ae4 100644 --- a/docs/reference/loadTimeToEventAnalyses.html +++ b/docs/reference/loadTimeToEventAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,13 +78,13 @@

Load the TimeToEvent results

- 
loadTimeToEventAnalyses(saveDirectory)
+ 
loadTimeToEventAnalyses(fileName)

Arguments

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -106,7 +106,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/runCharacterizationAnalyses.html b/docs/reference/runCharacterizationAnalyses.html index cbd1111..416f975 100644 --- a/docs/reference/runCharacterizationAnalyses.html +++ b/docs/reference/runCharacterizationAnalyses.html @@ -18,7 +18,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -177,7 +177,7 @@

Details

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/saveAggregateCovariateAnalyses.html b/docs/reference/saveAggregateCovariateAnalyses.html index 4083254..db5c47a 100644 --- a/docs/reference/saveAggregateCovariateAnalyses.html +++ b/docs/reference/saveAggregateCovariateAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,7 +78,7 @@

Save the AggregateCovariate results

- 
saveAggregateCovariateAnalyses(result, saveDirectory)
+ 
saveAggregateCovariateAnalyses(result, fileName)
@@ -87,8 +87,8 @@

Arguments

The output of running computeAggregateCovariateAnalyses()

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -110,7 +110,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/saveCharacterizationSettings.html b/docs/reference/saveCharacterizationSettings.html index 452c3df..34ec74e 100644 --- a/docs/reference/saveCharacterizationSettings.html +++ b/docs/reference/saveCharacterizationSettings.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,7 +78,7 @@

Save the characterization settings as a json

- 
saveCharacterizationSettings(settings, saveDirectory)
+ 
saveCharacterizationSettings(settings, fileName)
@@ -87,7 +87,7 @@

Arguments

An object of class characterizationSettings created using createCharacterizationSettings

-
saveDirectory
+
fileName

The location to save the json settings

@@ -114,7 +114,7 @@

Details

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/saveDechallengeRechallengeAnalyses.html b/docs/reference/saveDechallengeRechallengeAnalyses.html index 1316456..9d465f3 100644 --- a/docs/reference/saveDechallengeRechallengeAnalyses.html +++ b/docs/reference/saveDechallengeRechallengeAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,7 +78,7 @@

Save the DechallengeRechallenge results

- 
saveDechallengeRechallengeAnalyses(result, saveDirectory)
+ 
saveDechallengeRechallengeAnalyses(result, fileName)
@@ -87,8 +87,8 @@

Arguments

The output of running computeDechallengeRechallengeAnalyses()

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -110,7 +110,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html index d56acd8..de8f8b5 100644 --- a/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html +++ b/docs/reference/saveRechallengeFailCaseSeriesAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,7 +78,7 @@

Save the RechallengeFailCaseSeries results

- 
saveRechallengeFailCaseSeriesAnalyses(result, saveDirectory)
+ 
saveRechallengeFailCaseSeriesAnalyses(result, fileName)
@@ -87,8 +87,8 @@

Arguments

The output of running computeRechallengeFailCaseSeriesAnalyses()

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -110,7 +110,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/saveTimeToEventAnalyses.html b/docs/reference/saveTimeToEventAnalyses.html index 3d69544..914af23 100644 --- a/docs/reference/saveTimeToEventAnalyses.html +++ b/docs/reference/saveTimeToEventAnalyses.html @@ -17,7 +17,7 @@ Characterization - 0.0.4 + 0.1.0 @@ -78,7 +78,7 @@

Save the TimeToEvent results

- 
saveTimeToEventAnalyses(result, saveDirectory)
+ 
saveTimeToEventAnalyses(result, fileName)
@@ -87,8 +87,8 @@

Arguments

The output of running computeTimeToEventAnalyses()

-
saveDirectory
-

An directory location to save the results into

+
fileName
+

The file to save the results into.

@@ -110,7 +110,7 @@

Value

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/viewCharacterization.html b/docs/reference/viewCharacterization.html new file mode 100644 index 0000000..eb0f2a4 --- /dev/null +++ b/docs/reference/viewCharacterization.html @@ -0,0 +1,128 @@ + +viewCharacterization - Interactively view the characterization results — viewCharacterization • Characterization + + +
+
+ + + +
+
+
+

viewCharacterization - Interactively view the characterization results

+ Source: R/ViewShiny.R + +
+ +
+

This is a shiny app for viewing interactive plots and tables

+
+ +
+ 
viewCharacterization(resultLocation, cohortDefinitionSet = NULL)
+
+ +
+

Arguments

+
resultLocation
+

The location of the results

+ + +
cohortDefinitionSet
+

The cohortDefinitionSet extracted using webAPI

+ +
+
+

Value

+ + +

Opens a shiny app for interactively viewing the results

+
+
+

Details

+

Input is the output of ...

+
+ +
+ +
+ + +
+

Developed by Jenna Reps, Patrick Ryan.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index cd00cad..a679701 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -108,4 +108,7 @@ /reference/saveTimeToEventAnalyses.html + + /reference/viewCharacterization.html +