diff --git a/DESCRIPTION b/DESCRIPTION index 101a5847..0147d065 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Strategus Type: Package Title: Coordinating and Executing Analytics Using HADES Modules -Version: 0.2.0 -Date: 2023-01-26 +Version: 0.2.1 +Date: 2023-01-29 Authors@R: c( person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut")), person("Anthony", "Sena", email = "sena@ohdsi.org", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index 4d70ca49..28d06f42 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +Strategus 0.2.1 +=============== +- Update SelfControlledCaseSeries Module to v0.4.1 + Strategus 0.2.0 =============== - Add functions for developers to help with renv.lock file validation (#69) diff --git a/docs/404.html b/docs/404.html index c6d3a44b..428362fd 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/articles/CreatingAnalysisSpecification.html b/docs/articles/CreatingAnalysisSpecification.html index 549f2723..cab08ea9 100644 --- a/docs/articles/CreatingAnalysisSpecification.html +++ b/docs/articles/CreatingAnalysisSpecification.html @@ -33,7 +33,7 @@ Strategus - 0.2.0 + 0.2.1 @@ -94,7 +94,7 @@

Creating Analysis Specification

Anthony G. Sena

-

2024-01-26

+

2024-01-29

Source: vignettes/CreatingAnalysisSpecification.Rmd @@ -125,7 +125,7 @@

Setting up your R environmentremotes::install_github("ohdsi/Characterization", ref = "v0.1.3") remotes::install_github("ohdsi/CohortIncidence", ref = "v3.3.0") remotes::install_github("ohdsi/CohortMethod", ref = "v5.2.0") -remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.1.0") +remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.1.1") remotes::install_github("ohdsi/PatientLevelPrediction", ref = "v6.3.6")
@@ -407,7 +407,7 @@

SelfControlledCaseSeries Modul cohort analysis for this study.

 library(SelfControlledCaseSeries)
-source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.4.0/SettingsFunctions.R")
+source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.4.1/SettingsFunctions.R")
 
 # Exposures-outcomes -----------------------------------------------------------
 negativeControlOutcomeIds <- ncoCohortSet$cohortId
diff --git a/docs/articles/CreatingModules.html b/docs/articles/CreatingModules.html
index d6feff31..2c30932e 100644
--- a/docs/articles/CreatingModules.html
+++ b/docs/articles/CreatingModules.html
@@ -33,7 +33,7 @@
       
       
         Strategus
-        0.2.0
+        0.2.1
@@ -94,7 +94,7 @@

Creating Strategus Modules

Anthony G. Sena

-

2024-01-26

+

2024-01-29

Source: vignettes/CreatingModules.Rmd diff --git a/docs/articles/ExecuteStrategus.html b/docs/articles/ExecuteStrategus.html index aa60c340..db42432b 100644 --- a/docs/articles/ExecuteStrategus.html +++ b/docs/articles/ExecuteStrategus.html @@ -33,7 +33,7 @@ Strategus - 0.2.0 + 0.2.1

@@ -94,7 +94,7 @@

Execute Strategus

Anthony G. Sena

-

2024-01-26

+

2024-01-29

Source: vignettes/ExecuteStrategus.Rmd diff --git a/docs/articles/IntroductionToStrategus.html b/docs/articles/IntroductionToStrategus.html index 3178368b..4ae1a497 100644 --- a/docs/articles/IntroductionToStrategus.html +++ b/docs/articles/IntroductionToStrategus.html @@ -33,7 +33,7 @@ Strategus - 0.2.0 + 0.2.1 @@ -94,7 +94,7 @@

Introduction to Strategus

Anthony G. Sena

-

2024-01-26

+

2024-01-29

Source: vignettes/IntroductionToStrategus.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 0f50f0d8..fa6455b2 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/authors.html b/docs/authors.html index aa212655..424de98e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/index.html b/docs/index.html index 311f4453..1f07ab80 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/news/index.html b/docs/news/index.html index affd7d35..edefda43 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 @@ -69,6 +69,10 @@

Changelog

Source: NEWS.md +
+

Strategus 0.2.1

+
  • Update SelfControlledCaseSeries Module to v0.4.1
    • +

Strategus 0.2.0

  • Add functions for developers to help with renv.lock file validation (#69)
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a7811836..d66c1d42 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -6,5 +6,5 @@ articles: CreatingModules: CreatingModules.html ExecuteStrategus: ExecuteStrategus.html IntroductionToStrategus: IntroductionToStrategus.html -last_built: 2024-01-26T22:27Z +last_built: 2024-01-29T15:41Z diff --git a/docs/pull_request_template.html b/docs/pull_request_template.html index c47c3877..93b0b8d9 100644 --- a/docs/pull_request_template.html +++ b/docs/pull_request_template.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1
diff --git a/docs/reference/Strategus-package.html b/docs/reference/Strategus-package.html index a93984a3..f355a44b 100644 --- a/docs/reference/Strategus-package.html +++ b/docs/reference/Strategus-package.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/addModuleSpecifications.html b/docs/reference/addModuleSpecifications.html index 161cdc53..9427df29 100644 --- a/docs/reference/addModuleSpecifications.html +++ b/docs/reference/addModuleSpecifications.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/addSharedResources.html b/docs/reference/addSharedResources.html index aeb109f4..31dc58c4 100644 --- a/docs/reference/addSharedResources.html +++ b/docs/reference/addSharedResources.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/compareLockFiles.html b/docs/reference/compareLockFiles.html index 2c80398d..75a281f1 100644 --- a/docs/reference/compareLockFiles.html +++ b/docs/reference/compareLockFiles.html @@ -19,7 +19,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/createCdmExecutionSettings.html b/docs/reference/createCdmExecutionSettings.html index f94a811d..a4c48204 100644 --- a/docs/reference/createCdmExecutionSettings.html +++ b/docs/reference/createCdmExecutionSettings.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/createEmptyAnalysisSpecificiations.html b/docs/reference/createEmptyAnalysisSpecificiations.html index 4ecd5bf1..fe812331 100644 --- a/docs/reference/createEmptyAnalysisSpecificiations.html +++ b/docs/reference/createEmptyAnalysisSpecificiations.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/createResultDataModels.html b/docs/reference/createResultDataModels.html index 02dc382b..8e129216 100644 --- a/docs/reference/createResultDataModels.html +++ b/docs/reference/createResultDataModels.html @@ -19,7 +19,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/createResultsExecutionSettings.html b/docs/reference/createResultsExecutionSettings.html index 6ea8638c..5b692c6d 100644 --- a/docs/reference/createResultsExecutionSettings.html +++ b/docs/reference/createResultsExecutionSettings.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/dot-nullList.html b/docs/reference/dot-nullList.html index 6c69ccbc..a3723d15 100644 --- a/docs/reference/dot-nullList.html +++ b/docs/reference/dot-nullList.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/ensureAllModulesInstantiated.html b/docs/reference/ensureAllModulesInstantiated.html index f7b5ac10..2357de98 100644 --- a/docs/reference/ensureAllModulesInstantiated.html +++ b/docs/reference/ensureAllModulesInstantiated.html @@ -23,7 +23,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/execute.html b/docs/reference/execute.html index 205a0598..1c52a8d2 100644 --- a/docs/reference/execute.html +++ b/docs/reference/execute.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/getModuleList.html b/docs/reference/getModuleList.html index b5f753f6..06108bae 100644 --- a/docs/reference/getModuleList.html +++ b/docs/reference/getModuleList.html @@ -18,7 +18,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 80523ba2..6a5f65bc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/lockFileToDataFrame.html b/docs/reference/lockFileToDataFrame.html index 62ecc9aa..ac0bd68c 100644 --- a/docs/reference/lockFileToDataFrame.html +++ b/docs/reference/lockFileToDataFrame.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/mandatoryPackages.html b/docs/reference/mandatoryPackages.html index 2ddcf91c..1e1b96d5 100644 --- a/docs/reference/mandatoryPackages.html +++ b/docs/reference/mandatoryPackages.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/retrieveConnectionDetails.html b/docs/reference/retrieveConnectionDetails.html index f080424a..fabb17c4 100644 --- a/docs/reference/retrieveConnectionDetails.html +++ b/docs/reference/retrieveConnectionDetails.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/runSchemaCreation.html b/docs/reference/runSchemaCreation.html index 87839bbc..9c8ff327 100644 --- a/docs/reference/runSchemaCreation.html +++ b/docs/reference/runSchemaCreation.html @@ -22,7 +22,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/storeConnectionDetails.html b/docs/reference/storeConnectionDetails.html index 7a0a965f..2d99b7ab 100644 --- a/docs/reference/storeConnectionDetails.html +++ b/docs/reference/storeConnectionDetails.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/suggestedPacakges.html b/docs/reference/suggestedPacakges.html index c627aff5..c8bc036a 100644 --- a/docs/reference/suggestedPacakges.html +++ b/docs/reference/suggestedPacakges.html @@ -17,7 +17,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/syncLockFile.html b/docs/reference/syncLockFile.html index 249ac3f1..215adc23 100644 --- a/docs/reference/syncLockFile.html +++ b/docs/reference/syncLockFile.html @@ -26,7 +26,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/unlockKeyring.html b/docs/reference/unlockKeyring.html index c249db6c..53d8d979 100644 --- a/docs/reference/unlockKeyring.html +++ b/docs/reference/unlockKeyring.html @@ -19,7 +19,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/validateLockFile.html b/docs/reference/validateLockFile.html index 72dbdf4e..96ef71bc 100644 --- a/docs/reference/validateLockFile.html +++ b/docs/reference/validateLockFile.html @@ -20,7 +20,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/verifyModuleInstallation.html b/docs/reference/verifyModuleInstallation.html index 233b25dd..cd1f6b56 100644 --- a/docs/reference/verifyModuleInstallation.html +++ b/docs/reference/verifyModuleInstallation.html @@ -29,7 +29,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/docs/reference/withModuleRenv.html b/docs/reference/withModuleRenv.html index e93bab0b..af426614 100644 --- a/docs/reference/withModuleRenv.html +++ b/docs/reference/withModuleRenv.html @@ -20,7 +20,7 @@ Strategus - 0.2.0 + 0.2.1 diff --git a/extras/ExecuteStrategusOnEunomia.R b/extras/ExecuteStrategusOnEunomia.R index 2e23fdf9..4adc266a 100644 --- a/extras/ExecuteStrategusOnEunomia.R +++ b/extras/ExecuteStrategusOnEunomia.R @@ -7,9 +7,9 @@ #Run the Eunomia study --------- # Set the folder & environment variable for module storage -moduleFolder <- "C:/temp/strategus/modules" +moduleFolder <- Sys.getenv("INSTANTIATED_MODULES_FOLDER") studyFolder <- "C:/temp/strategus/EunomiaTestStudy" -Sys.setenv("INSTANTIATED_MODULES_FOLDER" = moduleFolder) + if (!dir.exists(moduleFolder)) { dir.create(moduleFolder, recursive = TRUE) @@ -66,7 +66,7 @@ executionSettings <- ParallelLogger::loadSettingsFromJson( Strategus::storeConnectionDetails( connectionDetails, - resultsConnectionDetailsReference + "eunomia" ) Strategus::createResultDataModels( diff --git a/extras/Strategus.pdf b/extras/Strategus.pdf index 0c6e3306..6fd84273 100644 Binary files a/extras/Strategus.pdf and b/extras/Strategus.pdf differ diff --git a/inst/csv/modules.csv b/inst/csv/modules.csv index 8198d685..3324247a 100644 --- a/inst/csv/modules.csv +++ b/inst/csv/modules.csv @@ -5,5 +5,5 @@ CohortGeneratorModule,v0.3.0,github.com,OHDSI,cdm,CohortGenerator,v0.8.1 CohortIncidenceModule,v0.4.0,github.com,OHDSI,cdm,CohortIncidence,v3.3.0 CohortMethodModule,v0.3.0,github.com,OHDSI,cdm,CohortMethod,v5.2.0 PatientLevelPredictionModule,v0.3.0,github.com,OHDSI,cdm,PatientLevelPrediction,v6.3.6 -SelfControlledCaseSeriesModule,v0.4.0,github.com,OHDSI,cdm,SelfControlledCaseSeries,v5.1.0 +SelfControlledCaseSeriesModule,v0.4.1,github.com,OHDSI,cdm,SelfControlledCaseSeries,v5.1.1 EvidenceSynthesisModule,v0.6.0,github.com,OHDSI,results,EvidenceSynthesis,v0.5.0 diff --git a/inst/doc/CreatingAnalysisSpecification.pdf b/inst/doc/CreatingAnalysisSpecification.pdf index 22471ddf..9ed3007f 100644 Binary files a/inst/doc/CreatingAnalysisSpecification.pdf and b/inst/doc/CreatingAnalysisSpecification.pdf differ diff --git a/inst/doc/CreatingModules.pdf b/inst/doc/CreatingModules.pdf index ae691b5c..2df5c663 100644 Binary files a/inst/doc/CreatingModules.pdf and b/inst/doc/CreatingModules.pdf differ diff --git a/inst/doc/ExecuteStrategus.pdf b/inst/doc/ExecuteStrategus.pdf index ef8d8425..1f70e6bb 100644 Binary files a/inst/doc/ExecuteStrategus.pdf and b/inst/doc/ExecuteStrategus.pdf differ diff --git a/inst/doc/IntroductionToStrategus.pdf b/inst/doc/IntroductionToStrategus.pdf index 978b632d..65bcb9fa 100644 Binary files a/inst/doc/IntroductionToStrategus.pdf and b/inst/doc/IntroductionToStrategus.pdf differ diff --git a/inst/testdata/analysisSpecification.json b/inst/testdata/analysisSpecification.json index bd4d6cb9..9c4557d0 100644 --- a/inst/testdata/analysisSpecification.json +++ b/inst/testdata/analysisSpecification.json @@ -1344,7 +1344,7 @@ }, { "module": "SelfControlledCaseSeriesModule", - "version": "0.4.0", + "version": "0.4.1", "remoteRepo": "github.com", "remoteUsername": "ohdsi", "settings": { @@ -2473,7 +2473,7 @@ "modelType": "logistic", "addIntercept": true, "useControl": true, - "seed": 17037306, + "seed": 15721621, "name": "Lasso Logistic Regression", "threads": -1, "tolerance": 2e-06, @@ -2488,7 +2488,7 @@ "splitSettings": { "test": 0.25, "train": 0.75, - "seed": 74734, + "seed": 78595, "nfold": 3, "attr_class": "splitSettings", "attr_fun": "randomSplitter" @@ -2610,7 +2610,7 @@ "modelType": "logistic", "addIntercept": true, "useControl": true, - "seed": 22792170, + "seed": 85843933, "name": "Lasso Logistic Regression", "threads": -1, "tolerance": 2e-06, @@ -2625,7 +2625,7 @@ "splitSettings": { "test": 0.25, "train": 0.75, - "seed": 14402, + "seed": 729, "nfold": 3, "attr_class": "splitSettings", "attr_fun": "randomSplitter" diff --git a/vignettes/CreatingAnalysisSpecification.Rmd b/vignettes/CreatingAnalysisSpecification.Rmd index bd8d0f1a..503a3311 100644 --- a/vignettes/CreatingAnalysisSpecification.Rmd +++ b/vignettes/CreatingAnalysisSpecification.Rmd @@ -47,7 +47,7 @@ remotes::install_github("ohdsi/CohortDiagnostics", ref = "v3.2.5") remotes::install_github("ohdsi/Characterization", ref = "v0.1.3") remotes::install_github("ohdsi/CohortIncidence", ref = "v3.3.0") remotes::install_github("ohdsi/CohortMethod", ref = "v5.2.0") -remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.1.0") +remotes::install_github("ohdsi/SelfControlledCaseSeries", ref = "v5.1.1") remotes::install_github("ohdsi/PatientLevelPrediction", ref = "v6.3.6") ``` @@ -310,7 +310,7 @@ The following code creates the `cohortMethodModuleSpecifications` to perform a c ```{r eval=FALSE} library(SelfControlledCaseSeries) -source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.4.0/SettingsFunctions.R") +source("https://raw.githubusercontent.com/OHDSI/SelfControlledCaseSeriesModule/v0.4.1/SettingsFunctions.R") # Exposures-outcomes ----------------------------------------------------------- negativeControlOutcomeIds <- ncoCohortSet$cohortId