From 19b8af0ae9d56b290c7e536c2d41ebb77365301e Mon Sep 17 00:00:00 2001
From: Anthony Sena Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.9. Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.9. Next we will use Next, we will use Finally, we can write out the execution settings to the file system
to capture this information. We recommend adding this environmental variable to your
And finally we execute the study: Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.9. Site built with pkgdown 2.0.7. Site built with pkgdown 2.0.9. A folder in the local file system where the module output will be written. Logging information from Strategus and all modules will be located in this file. Individual modules will continue to have their own module-specific logs. By default this will be written to the root of the The minimum number of subjects contributing to a count before it can be included
in results. A folder in the local file system where the module output will be written. Logging information from Strategus and all modules will be located in this file. Individual modules will continue to have their own module-specific logs. By default this will be written to the root of the The minimum number of subjects contributing to a count before it can be included
in results. When set to TRUE, Strategus will enforce
+module dependencies that are declared by each module. For example, the
+CohortDiagnostics module declares a dependency on the CohortGenerator module
+and Strategus will require that an analysis specification declare that both
+modules must exist in order to execute the analysis. When set to FALSE,
+Strategus will not enforce these module dependencies which assumes you have
+properly run all module dependencies yourself. Setting this to FALSE is not
+recommended since it is potentially unsafe. Restart run? Requires When set to TRUE, Strategus will enforce
+module dependencies that are declared by each module. For example, the
+CohortDiagnostics module declares a dependency on the CohortGenerator module
+and Strategus will require that an analysis specification declare that both
+modules must exist in order to execute the analysis. When set to FALSE,
+Strategus will not enforce these module dependencies which assumes you have
+properly run all module dependencies yourself. Setting this to FALSE is not
+recommended since it is potentially unsafe.Page not found (404)
diff --git a/docs/articles/CreatingAnalysisSpecification.html b/docs/articles/CreatingAnalysisSpecification.html
index cab08ea9..e2cef9fa 100644
--- a/docs/articles/CreatingAnalysisSpecification.html
+++ b/docs/articles/CreatingAnalysisSpecification.html
@@ -6,7 +6,7 @@
Creating Analysis Specification
Anthony G.
Sena
- 2024-01-29
+ 2024-06-04
Source: vignettes/CreatingAnalysisSpecification.Rmd
CreatingAnalysisSpecification.Rmd
Setting up your R environment
# Install correct versions of HADES packages
-remotes::install_github("ohdsi/CohortGenerator", ref = "v0.8.1")
+remotes::install_github("ohdsi/CohortGenerator", ref = "v0.9.0")
remotes::install_github("ohdsi/CohortDiagnostics", ref = "v3.2.5")
-remotes::install_github("ohdsi/Characterization", ref = "v0.1.3")
+remotes::install_github("ohdsi/Characterization", ref = "v0.2.0")
remotes::install_github("ohdsi/CohortIncidence", ref = "v3.3.0")
-remotes::install_github("ohdsi/CohortMethod", ref = "v5.2.0")
-remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.1.1")
+remotes::install_github("ohdsi/CohortMethod", ref = "v5.3.0")
+remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.2.0")
remotes::install_github("ohdsi/PatientLevelPrediction", ref = "v6.3.6")
CohortGenerator Module SettingscohortGeneratorModuleSpecifications function to specify the
cohort generation settings.
-
source("https://raw.githubusercontent.com/OHDSI/CohortGeneratorModule/v0.3.0/SettingsFunctions.R")
+
source("https://raw.githubusercontent.com/OHDSI/CohortGeneratorModule/v0.4.1/SettingsFunctions.R")
# Create the cohort definition shared resource element for the analysis specification
cohortDefinitionSharedResource <- createCohortSharedResourceSpecifications(
@@ -238,7 +238,7 @@
to perform an incidence
rate analysis for the target cohorts and outcome in this study.
CohortIncidence Module SettingscohortIncidenceModuleSpecifications
-
source("https://raw.githubusercontent.com/OHDSI/CohortIncidenceModule/v0.4.0/SettingsFunctions.R")
+
source("https://raw.githubusercontent.com/OHDSI/CohortIncidenceModule/v0.4.1/SettingsFunctions.R")
library(CohortIncidence)
targets <- list(
createCohortRef(id = 1, name = "Celecoxib"),
@@ -281,7 +281,7 @@
Characterization Module Settings
-
source("https://raw.githubusercontent.com/OHDSI/CharacterizationModule/v0.5.0/SettingsFunctions.R")
+
source("https://raw.githubusercontent.com/OHDSI/CharacterizationModule/v0.6.0/SettingsFunctions.R")
characterizationModuleSpecifications <- createCharacterizationModuleSpecifications(
targetIds = c(1, 2),
outcomeIds = 3,
@@ -304,7 +304,7 @@
CohortMethod Module Settings
library(CohortMethod)
-source("https://raw.githubusercontent.com/OHDSI/CohortMethodModule/v0.3.0/SettingsFunctions.R")
+source("https://raw.githubusercontent.com/OHDSI/CohortMethodModule/v0.3.1/SettingsFunctions.R")
negativeControlOutcomes <- lapply(
X = ncoCohortSet$cohortId,
FUN = createOutcome,
@@ -407,7 +407,7 @@
SelfControlledCaseSeries Modul
cohort analysis for this study.
library(SelfControlledCaseSeries)
-source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.4.1/SettingsFunctions.R")
+source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.5.0/SettingsFunctions.R")
# Exposures-outcomes -----------------------------------------------------------
negativeControlOutcomeIds <- ncoCohortSet$cohortId
@@ -602,7 +602,7 @@
Strategus Analysis Specifications
-
Creating Strategus Modules
Anthony G.
Sena
- 2024-01-29
+ 2024-06-04
Source: vignettes/CreatingModules.Rmd
CreatingModules.Rmd
Test Files
-
Execute Strategus
Anthony G.
Sena
- 2024-01-29
+ 2024-06-04
Source: vignettes/ExecuteStrategus.Rmd
ExecuteStrategus.Rmd
Storing the connection detailsconnectionDetails <- Eunomia::getEunomiaConnectionDetails(
databaseFile = file.path(outputFolder, "cdm.sqlite")
)
+## attempting to download GiBleed
## attempting to extract and load: D:/eunomiaData/GiBleed_5.3.zip to: D:/eunomiaData/GiBleed_5.3.sqlite
Strategus
to store the connection
details and provide a connectionDetailsReference
that
Strategus will use to look up the connection details.
+
storeConnectionDetails(
connectionDetails = connectionDetails,
connectionDetailsReference = "eunomia"
@@ -159,7 +161,7 @@
Creating an execution settings ob
Strategus
to create the CDM execution
settings. The connectionDetailsReference
refers to the
connection details we stored earlier:
+
executionSettings <- createCdmExecutionSettings(
connectionDetailsReference = "eunomia",
workDatabaseSchema = "main",
@@ -171,7 +173,7 @@
Creating an execution settings ob
)
+
ParallelLogger::saveSettingsToJson(
object = executionSettings,
file.path(outputFolder, "eunomiaExecutionSettings.json")
@@ -191,7 +193,7 @@
Specifying the instantiated
time-consuming task. We must specify a global location where these
modules will be instantiated so that, once a module is instantiated, it
can be used in all future studies:
-
+
Sys.setenv("INSTANTIATED_MODULES_FOLDER" = "c:/strategus/modules")
.renviron
file, so it is always set.Running the study
+
analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
fileName = system.file("testdata/analysisSpecification.json",
package = "Strategus"
@@ -212,7 +214,7 @@
Running the study= file.path(outputFolder, "eunomiaExecutionSettings.json")
)
+
execute(
analysisSpecifications = analysisSpecifications,
executionSettings = executionSettings,
@@ -244,7 +246,7 @@
Running the study
-
Introduction to Strategus
Anthony G.
Sena
- 2024-01-29
+ 2024-06-04
Source: vignettes/IntroductionToStrategus.Rmd
IntroductionToStrategus.Rmd
What is a HADES module?
-
All vignettes
Developers
diff --git a/docs/news/index.html b/docs/news/index.html
index edefda43..6d16928e 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog
Source: NEWS.md
+
Strategus 0.2.1
Strategus 0.0.1
Author
diff --git a/docs/reference/addModuleSpecifications.html b/docs/reference/addModuleSpecifications.html
index 9427df29..27bf3b31 100644
--- a/docs/reference/addModuleSpecifications.html
+++ b/docs/reference/addModuleSpecifications.html
@@ -1,5 +1,5 @@
-Value
diff --git a/docs/reference/addSharedResources.html b/docs/reference/addSharedResources.html
index 31dc58c4..14c5998c 100644
--- a/docs/reference/addSharedResources.html
+++ b/docs/reference/addSharedResources.html
@@ -1,5 +1,5 @@
-Value
diff --git a/docs/reference/compareLockFiles.html b/docs/reference/compareLockFiles.html
index 75a281f1..ecb363ca 100644
--- a/docs/reference/compareLockFiles.html
+++ b/docs/reference/compareLockFiles.html
@@ -1,5 +1,5 @@
-Create CDM execution settings
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
workFolder,
resultsFolder,
+ logFileName = file.path(resultsFolder, "strategus-log.txt"),
minCellCount = 5,
integerAsNumeric = getOption("databaseConnectorIntegerAsNumeric", default = TRUE),
integer64AsNumeric = getOption("databaseConnectorInteger64AsNumeric", default = TRUE),
@@ -126,6 +127,10 @@ Arguments
resultsFolder
Value
diff --git a/docs/reference/createEmptyAnalysisSpecificiations.html b/docs/reference/createEmptyAnalysisSpecificiations.html
index fe812331..10fbe085 100644
--- a/docs/reference/createEmptyAnalysisSpecificiations.html
+++ b/docs/reference/createEmptyAnalysisSpecificiations.html
@@ -1,5 +1,5 @@
-Value
diff --git a/docs/reference/createResultDataModels.html b/docs/reference/createResultDataModels.html
index 8e129216..a2563a20 100644
--- a/docs/reference/createResultDataModels.html
+++ b/docs/reference/createResultDataModels.html
@@ -1,5 +1,5 @@
-Create Results execution settings
resultsDatabaseSchema,
workFolder,
resultsFolder,
+ logFileName = file.path(resultsFolder, "strategus-log.txt"),
minCellCount = 5,
integerAsNumeric = getOption("databaseConnectorIntegerAsNumeric", default = TRUE),
integer64AsNumeric = getOption("databaseConnectorInteger64AsNumeric", default = TRUE)
@@ -105,6 +106,10 @@ Arguments
resultsFolder
Value
diff --git a/docs/reference/dot-nullList.html b/docs/reference/dot-nullList.html
index a3723d15..4aa0444f 100644
--- a/docs/reference/dot-nullList.html
+++ b/docs/reference/dot-nullList.html
@@ -1,5 +1,5 @@
-Used when serializing connection details to retain NULL values
diff --git a/docs/reference/ensureAllModulesInstantiated.html b/docs/reference/ensureAllModulesInstantiated.html
index 2357de98..1002ff06 100644
--- a/docs/reference/ensureAllModulesInstantiated.html
+++ b/docs/reference/ensureAllModulesInstantiated.html
@@ -1,5 +1,5 @@
-Ensure all modules are instantiated
ensureAllModulesInstantiated(analysisSpecifications, forceVerification = FALSE)
ensureAllModulesInstantiated(
+ analysisSpecifications,
+ forceVerification = FALSE,
+ enforceModuleDependencies = TRUE
+)
Arguments
the hash value of the module's renv.lock file in the file system so it can
by-pass running this check every time.
+
+Value
@@ -126,7 +141,7 @@ Value
Execute analysis specifications.
executionSettings,
executionScriptFolder = NULL,
keyringName = NULL,
- restart = FALSE
+ restart = FALSE,
+ enforceModuleDependencies = TRUE
)
@@ -115,6 +116,17 @@ Arguments
executionScriptFolder
to be specified, and be
the same as the executionScriptFolder
used in the run to restart.Value
@@ -136,7 +148,7 @@ Value
All functions
getModuleList()
Provides a list of HADES modules to run through Strategus
Install the latest release of a module
Synchronize renv.lock files and overwrite the target file -(read the description)
Synchronize renv.lock files and overwrite the target file (read the description)
Load module execution space inside and renv -inspired by targets::tar_script but allowing custom variable execution
Load module execution space inside and renv inspired by targets::tar_script but allowing custom variable execution
Create a zip file with all study results for sharing with study coordinator
R/ModuleInstantiation.R
+ installLatestModule.Rd
This function will call out to the OHDSI GitHub repo to find the latest
+version of the module and attempt to install it. Only modules that are listed
+in the getModuleList()
function are allowed since it will have a known
+GitHub location.
installLatestModule(moduleName)
The name of the module to install (i.e. "CohortGeneratorModule").
+This parameter must match a value found in the module
column of getModuleList()
None - this function is called for its side effects
+R/RenvHelpers.R
syncLockFile.Rd
R/ShareResults.R
+ zipResults.Rd
Create a zip file with all study results for sharing with study coordinator
+zipResults(resultsFolder, zipFile)
The folder holding the study results. This is found in
+executionSettings$resultsFolder
.
The path to the zip file to be created.
Does not return anything. Is called for the side-effect of creating the +zip file with results.
+Creates a .zip
file of the .csv
files found in the
+resultsFolder
. The resulting .zip
file will have
+relative paths to the root of the resultsFolder
+which is generally found in executionSettings$resultsFolder
.
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