From 311e7c6944d82b9ab9da0bd7d856a975fa5a55b9 Mon Sep 17 00:00:00 2001
From: Jamie Gilbert To publish with a config you can use: And press the publish button in the shiny app that loads. Note - that
+in this situation the use of secure keys with keyring is not
+possible. Site built with pkgdown 2.0.5. Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.5. Site built with pkgdown 2.0.7. If running the application from a R-studio environment, please make
sure the sqlite file is in a folder called ‘data’. Publishing the shiny app to a shared posit connect source can be
+achieved by first setting up credentials for your server.
+You will need to contact your internal administrator for publishing and
+access rights. Alternatively, you can use the shinyapps.io service,
+which provides some limited free usage for hosting your
+applications. Firstly, it is advised that you update to the latest version of OHDSI
+shiny modules with: This will update the dependencies for your shiny app. Following this you will need a copyable resource for your shiny app.
+This can be achieved by launching the This will create a shiny app folder
+ Publish button After this you can follow the RStudio prompts to upload to your
+rsconnect/posit connect or shinyapps.io server. To automatically create a zip archive containing the
This archive will contain a fully executable shiny application. Site built with pkgdown 2.0.5. Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.5. Site built with pkgdown 2.0.7. Rao G, Schuemie M, Ryan P, Weaver J, Gilbert J (2022).
+ Rao G, Schuemie M, Ryan P, Weaver J, Gilbert J (2023).
CohortDiagnostics: Diagnostics for OHDSI Cohorts.
https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics.
Added requirement for Andromeda 0.6.0 (which is implicitly required by DatabaseConnector) Fixed issue saving cohort subsets to csv file for viewing and analysis in shiny app Do not run orphan concepts checks for any subset cohorts Remove use of lookback period for IR calculations - this is now a setting of the call to the package Added data migration to support subsets in database schema (allow future functionality to take care of them) Added functionality to Moved most shiny code to Page not found (404)
diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html
index 2950d8852..a8f84602e 100644
--- a/docs/articles/CreatingAStudyPackage.html
+++ b/docs/articles/CreatingAStudyPackage.html
@@ -33,7 +33,7 @@
@@ -97,7 +97,7 @@ Creating a study package
Gowtham A.
Rao
- 2022-12-19
+ 2023-04-10
Source: vignettes/CreatingAStudyPackage.Rmd
CreatingAStudyPackage.Rmd
option A: Using Hydra and ROhdsiW
################# end of user input ##############
-webApiCohorts <- ROhdsiWebApi::getCohortDefinitionsMetaData(baseUrl = baseUrl)
+webApiCohorts <- ROhdsiWebApi::getCohortDefinitionsMetaData(baseUrl = baseUrl)
studyCohorts <- webApiCohorts %>%
dplyr::filter(.data$id %in% cohortIds)
@@ -237,7 +237,7 @@
option A: Using Hydra and ROhdsiW
cohortDefinitionsArray <- list()
for (i in (1:nrow(studyCohorts))) {
cohortDefinition <-
- ROhdsiWebApi::getCohortDefinition(
+ ROhdsiWebApi::getCohortDefinition(
cohortId = studyCohorts$id[[i]],
baseUrl = baseUrl
)
@@ -341,7 +341,7 @@
option A: Using Hydra and ROhdsiW
diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
index 409421e5e..8137b46fc 100644
--- a/docs/articles/DatabaseModeInDiagnosticsExplorer.html
+++ b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
@@ -33,7 +33,7 @@
@@ -97,7 +97,7 @@
Database mode in Diagnostics Explorer
Gowtham
Rao
- 2022-12-19
+ 2023-04-10
Source: vignettes/DatabaseModeInDiagnosticsExplorer.Rmd
DatabaseModeInDiagnosticsExplorer.Rmd
Database mode# If you wish to enable annotation - not currently reccomended in multi-user environments
enableAnnotation: FALSE
enableAuthorization: FALSE
+
+
Publishing
+
+
+
launchDiagnosticsExplorer(
+ shinyConfigPath = "path/to/config.yml",
+ makePublishable = TRUE,
+ publishDir = file.path(getwd(), "MyStudyDiagnosticsExplorer"),
+ overwritePublishDir = TRUE
+)
Database mode
-
Running Cohort Diagnostics
Gowtham Rao and
James P. Gilbert
- 2022-12-19
+ 2023-04-10
Source: vignettes/RunningCohortDiagnostics.Rmd
RunningCohortDiagnostics.Rmd
Loading cohort references from We
# list of cohort ids
cohortIds <- c(18345, 18346)
-cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(
+cohortDefinitionSet <- ROhdsiWebApi::exportCohortDefinitionSet(
baseUrl = baseUrl,
cohortIds = cohortIds,
generateStats = TRUE
@@ -336,7 +336,7 @@
Creating an sqlite db file
-
Viewing results using Diagnostics Explorer
Gowtham
Rao
- 2022-12-19
+ 2023-04-10
Source: vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd
ViewingResultsUsingDiagnosticsExplorer.Rmd
Running the app using
launchDiagnosticsExplorer(sqliteDbPath = "MyCohortDiagnosticsResulst.sqlite")
Publishing to Posit Connect or shinyapps.io
+
+
+remotes::install_packages('OHDSI/OhdsiShinyModules')
DiagnosticsExplorer
+with publishable options
+
launchDiagnosticsExplorer(
+ sqliteDbPath = "MyCohortDiagnosticsResulst.sqlite",
+ makePublishable = TRUE,
+ publishDir = file.path(getwd(), "MyStudyDiagnosticsExplorer"),
+ overwritePublishDir = TRUE
+)
"MyStudyDiagnosticsExplorer"
in your R working directory.
+The above will also overwrite the existing application folder and copy
+your sqlite file in to it. Following this, the shiny window should load
+and show a “publsh” button.Sharing a zipped copy of your shiny app
+
DiagnosticsExplorer
shiny application for deployment on
shared environments, such as data.ohdsi.org, run the function
createDiagnosticsExplorerZip
:
+
createDiagnosticsExplorerZip(outputZipfile = "MyCdProject.zip", sqliteDbPath = "MyCohortDiagnosticsResulst.sqlite")
Running over the network
-
What is Cohort Diagnostics?
Gowtham
Rao
- 2022-12-19
+ 2023-04-10
Source: vignettes/WhatIsCohortDiagnostics.Rmd
WhatIsCohortDiagnostics.Rmd
Features
-
All vignettes
diff --git a/docs/authors.html b/docs/authors.html
index 23ae44098..47e0c90c2 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
@@ -106,14 +106,14 @@ Citation
- @Manual{,
title = {CohortDiagnostics: Diagnostics for OHDSI Cohorts},
author = {Gowtham Rao and Martijn Schuemie and Patrick Ryan and James Weaver and Jamie Gilbert},
- year = {2022},
+ year = {2023},
note = {https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics},
}
@@ -128,7 +128,7 @@ Citation
diff --git a/docs/index.html b/docs/index.html
index f996a2927..901cdbcfe 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -39,7 +39,7 @@
@@ -102,7 +102,7 @@
Developers
Dev status
diff --git a/docs/news/index.html b/docs/news/index.html
index d57c4df65..21d45580b 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
@@ -72,6 +72,19 @@ Changelog
Source: NEWS.md
+ CohortDiagnostics 3.2.1
+CohortDiagnostics 3.2.0
+launchDiagnosticsExplorer
to make publishing to poist connect/shinyapps.io more straightforward (still requires removal of ggiraph)OHDSI/OhdsiShinyModules
Author
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html
index 65764abf8..89d24d0c5 100644
--- a/docs/reference/checkInputFileEncoding.html
+++ b/docs/reference/checkInputFileEncoding.html
@@ -18,7 +18,7 @@
@@ -108,7 +108,7 @@ Value
diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html
index e80a6695b..d44eeebe6 100644
--- a/docs/reference/createDiagnosticsExplorerZip.html
+++ b/docs/reference/createDiagnosticsExplorerZip.html
@@ -20,7 +20,7 @@
@@ -125,7 +125,7 @@ Arguments
diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html
index a9f04e857..1b3a384a8 100644
--- a/docs/reference/createMergedResultsFile.html
+++ b/docs/reference/createMergedResultsFile.html
@@ -19,7 +19,7 @@
@@ -124,7 +124,7 @@ Arguments
diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html
index 1ef9b5d09..ea7320c7f 100644
--- a/docs/reference/createResultsDataModel.html
+++ b/docs/reference/createResultsDataModel.html
@@ -17,7 +17,7 @@
@@ -116,7 +116,7 @@ Details
diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html
index c902b770b..e626d6ed5 100644
--- a/docs/reference/executeDiagnostics.html
+++ b/docs/reference/executeDiagnostics.html
@@ -22,7 +22,7 @@
@@ -116,6 +116,7 @@ Execute cohort diagnostics
temporalCovariateSettings = getDefaultCovariateSettings(),
minCellCount = 5,
minCharacterizationMean = 0.01,
+ irWashoutPeriod = 0,
incremental = FALSE,
incrementalFolder = file.path(exportFolder, "incremental")
)
@@ -254,6 +255,10 @@ Arguments
on covariates that have very low values. The default is 0.001 (i.e. 0.1 percent)
Number of days washout to include in calculation of incidence rates - default is 0
Create only cohort diagnostics that haven't been created before?
(optional) Only used if runOverNetwork
= TRUE.
(Optional) copy data files to make app publishable to posit connect/shinyapp.io
If make publishable is true - the directory that the shiny app is copied to
(Optional) If make publishable is true - overwrite the directory for publishing
Should the app be launched in your default browser, or in a Shiny window. Note: copying to clipboard will not work in a Shiny window.
(Optional) string to insert before table names (e.g. "cd_") for database table names
See ResultModelManager::uploadResults
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