diff --git a/Rmd/index.Rmd b/Rmd/index.Rmd index 1ab4673..ab8eb40 100644 --- a/Rmd/index.Rmd +++ b/Rmd/index.Rmd @@ -24,7 +24,7 @@ See the Support section for instructions on [setting up the R environment](rSetu ## Technology -HADES is a set of R packages that execute against data in a database server. HADES supports traditional database systems (PostgreSQL, Microsoft SQL Server, and Oracle), parallel data warehouses (Microsoft APS, IBM Netezza, and Amazon RedShift), as well as 'Big Data' platforms (Hadoop through Apache Impala, Apache Spark, and Google BigQuery). HADES does *not* support MySQL. +HADES is a set of R packages that execute against data in a database server. HADES supports traditional database systems (PostgreSQL, Microsoft SQL Server, and Oracle), parallel data warehouses (e.g. Amazon RedShift), as well as 'Big Data' platforms (e.g. Google BigQuery). HADES does *not* support MySQL. The full list of supported database platforms can be found [here](supportedPlatforms.html). ## License diff --git a/Rmd/installingHades.Rmd b/Rmd/installingHades.Rmd index d440220..8b59325 100644 --- a/Rmd/installingHades.Rmd +++ b/Rmd/installingHades.Rmd @@ -35,4 +35,21 @@ options(install.packages.compile.from.source = "never") library(remotes) update_packages() -``` \ No newline at end of file +``` + +# HADES-wide releases + +At the end of quarter 1 and 3 of each year a HADES-wide release is created. This is a snapshot of all HADES packages and their dependencies at one point in time. Additional checks are executed to ensure all packages and their dependencies work together. As such, these HADES-wide releases form a stable foundation for studies that may not require the absolute cutting-edge in HADES functionality. + +These releases are currently captured as [renv](https://rstudio.github.io/renv/articles/renv.html) lock files. The following releases are available: + +- 2023Q1: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q1/renv.lock) +- 2023Q3: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock) + +To build the R library corresponding to the latest release in your current RStudio project, you can use: + +```r +download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock", "renv.lock") +install.packages("renv") +renv::restore() +``` diff --git a/docs/index.html b/docs/index.html index 992cabf..7ec4bee 100644 --- a/docs/index.html +++ b/docs/index.html @@ -483,10 +483,10 @@

Learn How to Use HADES

Technology

HADES is a set of R packages that execute against data in a database server. HADES supports traditional database systems (PostgreSQL, -Microsoft SQL Server, and Oracle), parallel data warehouses (Microsoft -APS, IBM Netezza, and Amazon RedShift), as well as ‘Big Data’ platforms -(Hadoop through Apache Impala, Apache Spark, and Google BigQuery). HADES -does not support MySQL.

+Microsoft SQL Server, and Oracle), parallel data warehouses (e.g. Amazon +RedShift), as well as ‘Big Data’ platforms (e.g. Google BigQuery). HADES +does not support MySQL. The full list of supported database +platforms can be found here.

License

diff --git a/docs/installingHades.html b/docs/installingHades.html index a6be915..3d9d600 100644 --- a/docs/installingHades.html +++ b/docs/installingHades.html @@ -482,6 +482,31 @@

Updating HADES

library(remotes) update_packages()
+
+

HADES-wide releases

+

At the end of quarter 1 and 3 of each year a HADES-wide release is +created. This is a snapshot of all HADES packages and their dependencies +at one point in time. Additional checks are executed to ensure all +packages and their dependencies work together. As such, these HADES-wide +releases form a stable foundation for studies that may not require the +absolute cutting-edge in HADES functionality.

+

These releases are currently captured as renv lock +files. The following releases are available:

+ +

To build the R library corresponding to the latest release in your +current RStudio project, you can use:

+
download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock", "renv.lock")
+install.packages("renv")
+renv::restore()
+
diff --git a/extras/Releasing/TestCohortDiagnostics.R b/extras/Releasing/TestCohortDiagnostics.R new file mode 100644 index 0000000..37dc04c --- /dev/null +++ b/extras/Releasing/TestCohortDiagnostics.R @@ -0,0 +1,106 @@ +# Unit tests on CohortDiagnostics using testing servers take too long, so using local +# Postgres server +library(dplyr) +library(Capr) + +connectionDetails <- DatabaseConnector::createConnectionDetails( + dbms = "postgresql", + user = Sys.getenv("LOCAL_POSTGRES_USER"), + password = Sys.getenv("LOCAL_POSTGRES_PASSWORD"), + server = Sys.getenv("LOCAL_POSTGRES_SERVER") +) +cdmDatabaseSchema <- Sys.getenv("LOCAL_POSTGRES_CDM_SCHEMA") +cohortDatabaseSchema <- Sys.getenv("LOCAL_POSTGRES_OHDSI_SCHEMA") +cohortTable <- "cd_test" +folder <- "e:/temp/cdOutput" + +# Create cohorts using Capr ---------------------------------------------------- +osteoArthritisOfKneeConceptId <- 4079750 +celecoxibConceptId <- 1118084 +diclofenacConceptId <- 1124300 +osteoArthritisOfKnee <- cs( + descendants(osteoArthritisOfKneeConceptId), + name = "Osteoarthritis of knee" +) +attrition = attrition( + "prior osteoarthritis of knee" = withAll( + atLeast(1, conditionOccurrence(osteoArthritisOfKnee), duringInterval(eventStarts(-Inf, 0))) + ) +) +celecoxib <- cs( + descendants(celecoxibConceptId), + name = "Celecoxib" +) +diclofenac <- cs( + descendants(diclofenacConceptId), + name = "Diclofenac" +) +celecoxibCohort <- cohort( + entry = entry( + drugExposure(celecoxib, firstOccurrence()), + observationWindow = continuousObservation(priorDays = 365) + ), + # attrition = attrition, + exit = exit(endStrategy = drugExit(celecoxib, + persistenceWindow = 30, + surveillanceWindow = 0)) +) +diclofenacCohort <- cohort( + entry = entry( + drugExposure(diclofenac, firstOccurrence()), + observationWindow = continuousObservation(priorDays = 365) + ), + # attrition = attrition, + exit = exit(endStrategy = drugExit(diclofenac, + persistenceWindow = 30, + surveillanceWindow = 0)) +) +cohortDefinitionSet <- Capr::makeCohortSet(celecoxibCohort, diclofenacCohort) + +# Generate cohorts ------------------------------------------------------------- +cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = cohortTable) +CohortGenerator::createCohortTables( + connectionDetails = connectionDetails, + cohortTableNames = cohortTableNames, + cohortDatabaseSchema = cohortDatabaseSchema, + incremental = FALSE +) +CohortGenerator::generateCohortSet( + connectionDetails = connectionDetails, + cdmDatabaseSchema = cdmDatabaseSchema, + cohortDatabaseSchema = cohortDatabaseSchema, + cohortTableNames = cohortTableNames, + cohortDefinitionSet = cohortDefinitionSet, + incremental = FALSE +) +CohortGenerator::getCohortCounts(connectionDetails = connectionDetails, + cohortDatabaseSchema = cohortDatabaseSchema, + cohortTable = cohortTable) + +# Run CohortDiagnostics -------------------------------------------------------- +dir.create(folder) + +cohortDefinitionSet$cohortId <- as.double(cohortDefinitionSet$cohortId) +CohortDiagnostics::executeDiagnostics( + cohortDefinitionSet = cohortDefinitionSet, + connectionDetails = connectionDetails, + cdmDatabaseSchema = cdmDatabaseSchema, + cohortDatabaseSchema = cohortDatabaseSchema, + cohortTable = cohortTable, + cohortIds = cohortDefinitionSet$cohortId, + exportFolder = file.path(folder, "export"), + databaseId = "Synpuf", + runInclusionStatistics = TRUE, + runBreakdownIndexEvents = TRUE, + runTemporalCohortCharacterization = TRUE, + runIncidenceRate = TRUE, + runIncludedSourceConcepts = TRUE, + runOrphanConcepts = TRUE, + runTimeSeries = TRUE, + runCohortRelationship = TRUE, + minCellCount = 5, +) + +file.exists(file.path( + folder, "export", paste0("Results_Synpuf.zip") +)) diff --git a/hadesWideReleases/2023Oct08/renv.lock b/hadesWideReleases/2023Oct08/renv.lock new file mode 100644 index 0000000..4160f8f --- /dev/null +++ b/hadesWideReleases/2023Oct08/renv.lock @@ -0,0 +1,1565 @@ +{ + "R" : { + "Version" : 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new file mode 100644 index 0000000..0bbbe33 --- /dev/null +++ b/hadesWideReleases/2023Q1/README.md @@ -0,0 +1,4 @@ +HADES-wide release Q1 2023 +========================== + +Note: this is the same lock file as [here](https://github.com/OHDSI/Hades/tree/main/hadesWideReleases/2023Mar30), just marking it as the official Q1 2023 release. \ No newline at end of file diff --git a/hadesWideReleases/2023Q1/renv.lock b/hadesWideReleases/2023Q1/renv.lock new file mode 100644 index 0000000..a54ad3f --- /dev/null +++ b/hadesWideReleases/2023Q1/renv.lock @@ -0,0 +1,1467 @@ +{ + "R" : { + "Version" : "4.2.3", + "Repositories" : [ + { + "Name" : "CRAN", + "URL" : "https://cloud.r-project.org" + } + ] + }, + "Packages" : { + "cli" : { + "Package" : "cli", + "Version" : "3.6.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "glue" : { + "Package" : "glue", + "Version" : "1.6.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "rlang" : { + "Package" : "rlang", + "Version" : 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"Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "FeatureExtraction", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v3.2.0" + }, + "CohortGenerator" : { + "Package" : "CohortGenerator", + "Version" : "0.8.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "CohortGenerator", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.8.0" + }, + "OhdsiShinyModules" : { + "Package" : "OhdsiShinyModules", + "Version" : "1.1.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "OhdsiShinyModules", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.1.0" + }, + "PatientLevelPrediction" : { + "Package" : "PatientLevelPrediction", + "Version" : "6.3.1", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "PatientLevelPrediction", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v6.3.1" + }, + "ResultModelManager" : { + "Package" : "ResultModelManager", + "Version" : "0.3.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "ResultModelManager", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.3.0" + }, + "BigKnn" : { + "Package" : "BigKnn", + "Version" : "1.0.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "BigKnn", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.0.2" + }, + "Capr" : { + "Package" : "Capr", + "Version" : "2.0.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "Capr", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v2.0.0" + }, + "Characterization" : { + "Package" : "Characterization", + "Version" : "0.1.1", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "Characterization", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.1.1" + }, + "CohortDiagnostics" : { + "Package" : "CohortDiagnostics", + "Version" : "3.1.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "CohortDiagnostics", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v3.1.2" + }, + "CohortExplorer" : { + "Package" : "CohortExplorer", + "Version" : "0.0.11", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "CohortExplorer", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.0.11" + }, + "CohortMethod" : { + "Package" : "CohortMethod", + "Version" : "4.2.3", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "CohortMethod", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v4.2.3" + }, + "DataQualityDashboard" : { + "Package" : "DataQualityDashboard", + "Version" : "2.1.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "DataQualityDashboard", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v2.1.2" + }, + "DeepPatientLevelPrediction" : { + "Package" : "DeepPatientLevelPrediction", + "Version" : "1.1.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "DeepPatientLevelPrediction", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.1.2" + }, + "EnsemblePatientLevelPrediction" : { + "Package" : "EnsemblePatientLevelPrediction", + "Version" : "1.0.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "EnsemblePatientLevelPrediction", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.0.2" + }, + "Eunomia" : { + "Package" : "Eunomia", + "Version" : "1.0.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "Eunomia", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.0.2" + }, + "Hydra" : { + "Package" : "Hydra", + "Version" : "0.4.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "Hydra", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.4.0" + }, + "MethodEvaluation" : { + "Package" : "MethodEvaluation", + "Version" : "2.2.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "MethodEvaluation", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v2.2.0" + }, + "OhdsiSharing" : { + "Package" : "OhdsiSharing", + "Version" : "0.2.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "OhdsiSharing", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v0.2.2" + }, + "PhenotypeLibrary" : { + "Package" : "PhenotypeLibrary", + "Version" : "3.12.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "PhenotypeLibrary", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v3.12.0" + }, + "PheValuator" : { + "Package" : "PheValuator", + "Version" : "2.2.2", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "PheValuator", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v2.2.2" + }, + "ROhdsiWebApi" : { + "Package" : "ROhdsiWebApi", + "Version" : "1.3.3", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "ROhdsiWebApi", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.3.3" + }, + "SelfControlledCaseSeries" : { + "Package" : "SelfControlledCaseSeries", + "Version" : "4.1.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "SelfControlledCaseSeries", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v4.1.0" + }, + "SelfControlledCohort" : { + "Package" : "SelfControlledCohort", + "Version" : "1.6.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "SelfControlledCohort", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.6.0" + }, + "ShinyAppBuilder" : { + "Package" : "ShinyAppBuilder", + "Version" : "1.1.1", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "ShinyAppBuilder", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.1.1" + }, + "Hades" : { + "Package" : "Hades", + "Version" : "1.11.0", + "Source" : "GitHub", + "RemoteType" : "github", + "RemoteHost" : "api.github.com", + "RemoteRepo" : "Hades", + "RemoteUsername" : "ohdsi", + "RemoteRef" : "v1.11.0" + } + } +} diff --git a/hadesWideReleases/2023Q3/README.md b/hadesWideReleases/2023Q3/README.md new file mode 100644 index 0000000..8542ca6 --- /dev/null +++ b/hadesWideReleases/2023Q3/README.md @@ -0,0 +1,4 @@ +HADES-wide release Q3 2023 +========================== + +Note: this is the same lock file as [here](https://github.com/OHDSI/Hades/tree/main/hadesWideReleases/2023Oct08), just marking it as the official Q3 2023 release. \ No newline at end of file diff --git a/hadesWideReleases/2023Q3/renv.lock b/hadesWideReleases/2023Q3/renv.lock index a54ad3f..4160f8f 100644 --- a/hadesWideReleases/2023Q3/renv.lock +++ b/hadesWideReleases/2023Q3/renv.lock @@ -23,7 +23,7 @@ }, "rlang" : { "Package" : "rlang", - "Version" : "1.1.0", + "Version" : "1.1.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -39,6 +39,18 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "ps" : { + "Package" : "ps", + "Version" : "1.7.5", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R6" : { + "Package" : "R6", + "Version" : "2.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, "utf8" : { "Package" : "utf8", "Version" : "1.2.3", @@ -47,7 +59,7 @@ }, "vctrs" : { "Package" : "vctrs", - "Version" : "0.6.1", + "Version" : "0.6.3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -59,7 +71,7 @@ }, "digest" : { "Package" : "digest", - "Version" : "0.6.31", + "Version" : "0.6.33", "Source" : "Repository", "Repository" : "CRAN" }, @@ -93,9 +105,21 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "processx" : { + "Package" : "processx", + "Version" : "3.8.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "rprojroot" : { + "Package" : "rprojroot", + "Version" : "2.0.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, "withr" : { "Package" : "withr", - "Version" : "2.5.0", + "Version" : "2.5.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -107,13 +131,19 @@ }, "cachem" : { "Package" : "cachem", - "Version" : "1.0.7", + "Version" : "1.0.8", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "callr" : { + "Package" : "callr", + "Version" : "3.7.3", "Source" : "Repository", "Repository" : "CRAN" }, "cpp11" : { "Package" : "cpp11", - "Version" : "0.4.3", + "Version" : "0.4.6", "Source" : "Repository", "Repository" : "CRAN" }, @@ -123,9 +153,15 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "desc" : { + "Package" : "desc", + "Version" : "1.4.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, "fs" : { "Package" : "fs", - "Version" : "1.6.1", + "Version" : "1.6.3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -143,25 +179,13 @@ }, "htmltools" : { "Package" : "htmltools", - "Version" : "0.5.5", + "Version" : "0.5.6", "Source" : "Repository", "Repository" : "CRAN" }, "prettyunits" : { "Package" : "prettyunits", - "Version" : "1.1.1", - "Source" : "Repository", - "Repository" : "CRAN" - }, - "ps" : { - "Package" : "ps", - "Version" : "1.7.3", - "Source" : "Repository", - "Repository" : "CRAN" - }, - "R6" : { - "Package" : "R6", - "Version" : "2.5.1", + "Version" : "1.2.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -173,13 +197,7 @@ }, "Rcpp" : { "Package" : "Rcpp", - "Version" : "1.0.10", - "Source" : "Repository", - "Repository" : "CRAN" - }, - "rprojroot" : { - "Package" : "rprojroot", - "Version" : "2.0.3", + "Version" : "1.0.11", "Source" : "Repository", "Repository" : "CRAN" }, @@ -203,7 +221,7 @@ }, "xfun" : { "Package" : "xfun", - "Version" : "0.38", + "Version" : "0.40", "Source" : "Repository", "Repository" : "CRAN" }, @@ -225,12 +243,6 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "desc" : { - "Package" : "desc", - "Version" : "1.4.2", - "Source" : "Repository", - "Repository" : "CRAN" - }, "diffobj" : { "Package" : "diffobj", "Version" : "0.3.5", @@ -239,13 +251,13 @@ }, "dplyr" : { "Package" : "dplyr", - "Version" : "1.1.1", + "Version" : "1.1.3", "Source" : "Repository", "Repository" : "CRAN" }, "evaluate" : { "Package" : "evaluate", - "Version" : "0.20", + "Version" : "0.22", "Source" : "Repository", "Repository" : "CRAN" }, @@ -263,13 +275,13 @@ }, "jsonlite" : { "Package" : "jsonlite", - "Version" : "1.8.4", + "Version" : "1.8.7", "Source" : "Repository", "Repository" : "CRAN" }, "later" : { "Package" : "later", - "Version" : "1.3.0", + "Version" : "1.3.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -291,9 +303,9 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "processx" : { - "Package" : "processx", - "Version" : "3.8.0", + "pkgbuild" : { + "Package" : "pkgbuild", + "Version" : "1.4.2", "Source" : "Repository", "Repository" : "CRAN" }, @@ -305,7 +317,7 @@ }, "purrr" : { "Package" : "purrr", - "Version" : "1.0.1", + "Version" : "1.0.2", "Source" : "Repository", "Repository" : "CRAN" }, @@ -317,7 +329,7 @@ }, "sass" : { "Package" : "sass", - "Version" : "0.4.5", + "Version" : "0.4.7", "Source" : "Repository", "Repository" : "CRAN" }, @@ -329,13 +341,13 @@ }, "sys" : { "Package" : "sys", - "Version" : "3.4.1", + "Version" : "3.4.2", "Source" : "Repository", "Repository" : "CRAN" }, "tzdb" : { "Package" : "tzdb", - "Version" : "0.3.0", + "Version" : "0.4.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -347,7 +359,7 @@ }, "askpass" : { "Package" : "askpass", - "Version" : "1.1", + "Version" : "1.2.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -365,19 +377,13 @@ }, "bslib" : { "Package" : "bslib", - "Version" : "0.4.2", - "Source" : "Repository", - "Repository" : "CRAN" - }, - "callr" : { - "Package" : "callr", - "Version" : "3.7.3", + "Version" : "0.5.1", "Source" : "Repository", "Repository" : "CRAN" }, "checkmate" : { "Package" : "checkmate", - "Version" : "2.1.0", + "Version" : "2.2.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -401,19 +407,19 @@ }, "fontawesome" : { "Package" : "fontawesome", - "Version" : "0.5.0", + "Version" : "0.5.2", "Source" : "Repository", "Repository" : "CRAN" }, "knitr" : { "Package" : "knitr", - "Version" : "1.42", + "Version" : "1.44", "Source" : "Repository", "Repository" : "CRAN" }, "labeling" : { "Package" : "labeling", - "Version" : "0.4.2", + "Version" : "0.4.3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -437,7 +443,7 @@ }, "pkgload" : { "Package" : "pkgload", - "Version" : "1.3.2", + "Version" : "1.3.3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -455,7 +461,7 @@ }, "promises" : { "Package" : "promises", - "Version" : "1.2.0.1", + "Version" : "1.2.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -479,7 +485,7 @@ }, "tinytex" : { "Package" : "tinytex", - "Version" : "0.44", + "Version" : "0.47", "Source" : "Repository", "Repository" : "CRAN" }, @@ -491,19 +497,25 @@ }, "viridisLite" : { "Package" : "viridisLite", - "Version" : "0.4.1", + "Version" : "0.4.2", "Source" : "Repository", "Repository" : "CRAN" }, "vroom" : { "Package" : "vroom", - "Version" : "1.6.1", + "Version" : "1.6.3", "Source" : "Repository", "Repository" : "CRAN" }, "waldo" : { "Package" : "waldo", - "Version" : "0.4.0", + "Version" : "0.5.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "zoo" : { + "Package" : "zoo", + "Version" : "1.8-12", "Source" : "Repository", "Repository" : "CRAN" }, @@ -521,25 +533,25 @@ }, "curl" : { "Package" : "curl", - "Version" : "5.0.0", + "Version" : "5.1.0", "Source" : "Repository", "Repository" : "CRAN" }, "dbplyr" : { "Package" : "dbplyr", - "Version" : "2.3.2", + "Version" : "2.3.4", "Source" : "Repository", "Repository" : "CRAN" }, "gtable" : { "Package" : "gtable", - "Version" : "0.3.3", + "Version" : "0.3.4", "Source" : "Repository", "Repository" : "CRAN" }, "httpuv" : { "Package" : "httpuv", - "Version" : "1.6.9", + "Version" : "1.6.11", "Source" : "Repository", "Repository" : "CRAN" }, @@ -575,7 +587,7 @@ }, "openssl" : { "Package" : "openssl", - "Version" : "2.0.6", + "Version" : "2.1.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -587,13 +599,13 @@ }, "rmarkdown" : { "Package" : "rmarkdown", - "Version" : "2.21", + "Version" : "2.25", "Source" : "Repository", "Repository" : "CRAN" }, "RSQLite" : { "Package" : "RSQLite", - "Version" : "2.3.0", + "Version" : "2.3.1", "Source" : "Repository", "Repository" : "CRAN" }, @@ -617,13 +629,13 @@ }, "SqlRender" : { "Package" : "SqlRender", - "Version" : "1.13.1", + "Version" : "1.16.1", "Source" : "Repository", "Repository" : "CRAN" }, "testthat" : { "Package" : "testthat", - "Version" : "3.1.7", + "Version" : "3.1.10", "Source" : "Repository", "Repository" : "CRAN" }, @@ -635,7 +647,7 @@ }, "xml2" : { "Package" : "xml2", - "Version" : "1.3.3", + "Version" : "1.3.5", "Source" : "Repository", "Repository" : "CRAN" }, @@ -645,9 +657,15 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "xts" : { + "Package" : "xts", + "Version" : "0.13.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, "zip" : { "Package" : "zip", - "Version" : "2.2.2", + "Version" : "2.3.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -669,12 +687,6 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "coro" : { - "Package" : "coro", - "Version" : "1.0.3", - "Source" : "Repository", - "Repository" : "CRAN" - }, "crosstalk" : { "Package" : "crosstalk", "Version" : "1.2.0", @@ -689,13 +701,19 @@ }, "DatabaseConnector" : { "Package" : "DatabaseConnector", - "Version" : "6.1.0", + "Version" : "6.2.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "formatR" : { + "Package" : "formatR", + "Version" : "1.14", "Source" : "Repository", "Repository" : "CRAN" }, "ggplot2" : { "Package" : "ggplot2", - "Version" : "3.4.1", + "Version" : "3.4.3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -713,7 +731,7 @@ }, "httr" : { "Package" : "httr", - "Version" : "1.4.5", + "Version" : "1.4.7", "Source" : "Repository", "Repository" : "CRAN" }, @@ -725,7 +743,7 @@ }, "minqa" : { "Package" : "minqa", - "Version" : "1.2.5", + "Version" : "1.2.6", "Source" : "Repository", "Repository" : "CRAN" }, @@ -743,19 +761,19 @@ }, "ParallelLogger" : { "Package" : "ParallelLogger", - "Version" : "3.1.0", + "Version" : "3.3.0", "Source" : "Repository", "Repository" : "CRAN" }, "pbapply" : { "Package" : "pbapply", - "Version" : "1.7-0", + "Version" : "1.7-2", "Source" : "Repository", "Repository" : "CRAN" }, "plyr" : { "Package" : "plyr", - "Version" : "1.8.8", + "Version" : "1.8.9", "Source" : "Repository", "Repository" : "CRAN" }, @@ -791,7 +809,7 @@ }, "shiny" : { "Package" : "shiny", - "Version" : "1.7.4", + "Version" : "1.7.5", "Source" : "Repository", "Repository" : "CRAN" }, @@ -807,6 +825,12 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "TTR" : { + "Package" : "TTR", + "Version" : "0.24.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, "assertthat" : { "Package" : "assertthat", "Version" : "0.2.1", @@ -819,15 +843,27 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "cowplot" : { + "Package" : "cowplot", + "Version" : "1.1.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, "Cyclops" : { "Package" : "Cyclops", - "Version" : "3.2.1", + "Version" : "3.3.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "distributional" : { + "Package" : "distributional", + "Version" : "0.3.2", "Source" : "Repository", "Repository" : "CRAN" }, "DT" : { "Package" : "DT", - "Version" : "0.27", + "Version" : "0.30", "Source" : "Repository", "Repository" : "CRAN" }, @@ -837,21 +873,39 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "futile.options" : { + "Package" : "futile.options", + "Version" : "1.0.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, "gridExtra" : { "Package" : "gridExtra", "Version" : "2.3", "Source" : "Repository", "Repository" : "CRAN" }, + "lambda.r" : { + "Package" : "lambda.r", + "Version" : "1.2.4", + "Source" : "Repository", + "Repository" : "CRAN" + }, "lme4" : { "Package" : "lme4", - "Version" : "1.1-32", + "Version" : "1.1-34", "Source" : "Repository", "Repository" : "CRAN" }, "lubridate" : { "Package" : "lubridate", - "Version" : "1.9.2", + "Version" : "1.9.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "markdown" : { + "Package" : "markdown", + "Version" : "1.9", "Source" : "Repository", "Repository" : "CRAN" }, @@ -863,19 +917,19 @@ }, "metafor" : { "Package" : "metafor", - "Version" : "4.0-0", + "Version" : "4.4-0", "Source" : "Repository", "Repository" : "CRAN" }, "plotly" : { "Package" : "plotly", - "Version" : "4.10.1", + "Version" : "4.10.2", "Source" : "Repository", "Repository" : "CRAN" }, "polspline" : { "Package" : "polspline", - "Version" : "1.1.22", + "Version" : "1.1.23", "Source" : "Repository", "Repository" : "CRAN" }, @@ -887,7 +941,7 @@ }, "pROC" : { "Package" : "pROC", - "Version" : "1.18.0", + "Version" : "1.18.4", "Source" : "Repository", "Repository" : "CRAN" }, @@ -897,6 +951,18 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "quadprog" : { + "Package" : "quadprog", + "Version" : "1.5-8", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "quantmod" : { + "Package" : "quantmod", + "Version" : "0.4.25", + "Source" : "Repository", + "Repository" : "CRAN" + }, "reactable" : { "Package" : "reactable", "Version" : "0.4.4", @@ -905,7 +971,7 @@ }, "reticulate" : { "Package" : "reticulate", - "Version" : "1.28", + "Version" : "1.32.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -923,13 +989,13 @@ }, "shinyWidgets" : { "Package" : "shinyWidgets", - "Version" : "0.7.6", + "Version" : "0.8.0", "Source" : "Repository", "Repository" : "CRAN" }, "sodium" : { "Package" : "sodium", - "Version" : "1.2.1", + "Version" : "1.3.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -939,12 +1005,6 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "torch" : { - "Package" : "torch", - "Version" : "0.9.1", - "Source" : "Repository", - "Repository" : "CRAN" - }, "BeastJar" : { "Package" : "BeastJar", "Version" : "1.10.6", @@ -953,7 +1013,7 @@ }, "clock" : { "Package" : "clock", - "Version" : "0.6.1", + "Version" : "0.7.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -969,6 +1029,18 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "futile.logger" : { + "Package" : "futile.logger", + "Version" : "1.4.3", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "ggdist" : { + "Package" : "ggdist", + "Version" : "3.3.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, "HDInterval" : { "Package" : "HDInterval", "Version" : "0.2.4", @@ -983,7 +1055,7 @@ }, "meta" : { "Package" : "meta", - "Version" : "6.2-1", + "Version" : "6.5-0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -999,15 +1071,39 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "torchopt" : { - "Package" : "torchopt", - "Version" : "0.1.3", + "remotes" : { + "Package" : "remotes", + "Version" : "2.4.2.1", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "tseries" : { + "Package" : "tseries", + "Version" : "0.10-54", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "Achilles" : { + "Package" : "Achilles", + "Version" : "1.7.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "BrokenAdaptiveRidge" : { + "Package" : "BrokenAdaptiveRidge", + "Version" : "1.0.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "CohortExplorer" : { + "Package" : "CohortExplorer", + "Version" : "0.0.17", "Source" : "Repository", "Repository" : "CRAN" }, "EvidenceSynthesis" : { "Package" : "EvidenceSynthesis", - "Version" : "0.4.0", + "Version" : "0.5.0", "Source" : "Repository", "Repository" : "CRAN" }, @@ -1025,13 +1121,13 @@ }, "broom" : { "Package" : "broom", - "Version" : "1.0.4", + "Version" : "1.0.5", "Source" : "Repository", "Repository" : "CRAN" }, "MatrixModels" : { "Package" : "MatrixModels", - "Version" : "0.5-1", + "Version" : "0.5-2", "Source" : "Repository", "Repository" : "CRAN" }, @@ -1067,7 +1163,7 @@ }, "quantreg" : { "Package" : "quantreg", - "Version" : "5.94", + "Version" : "5.97", "Source" : "Repository", "Repository" : "CRAN" }, @@ -1089,18 +1185,6 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "markdown" : { - "Package" : "markdown", - "Version" : "1.5", - "Source" : "Repository", - "Repository" : "CRAN" - }, - "cowplot" : { - "Package" : "cowplot", - "Version" : "1.1.1", - "Source" : "Repository", - "Repository" : "CRAN" - }, "exactRankTests" : { "Package" : "exactRankTests", "Version" : "0.8-35", @@ -1145,7 +1229,7 @@ }, "mvtnorm" : { "Package" : "mvtnorm", - "Version" : "1.1-3", + "Version" : "1.2-3", "Source" : "Repository", "Repository" : "CRAN" }, @@ -1161,12 +1245,6 @@ "Source" : "Repository", "Repository" : "CRAN" }, - "zoo" : { - "Package" : "zoo", - "Version" : "1.8-11", - "Source" : "Repository", - "Repository" : "CRAN" - }, "ggpubr" : { "Package" : "ggpubr", "Version" : "0.6.0", @@ -1197,31 +1275,61 @@ "Source" : "Repository", "Repository" : "CRAN" }, + "aws.signature" : { + "Package" : "aws.signature", + "Version" : "0.6.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "aws.s3" : { + "Package" : "aws.s3", + "Version" : "0.3.21", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R.methodsS3" : { + "Package" : "R.methodsS3", + "Version" : "1.8.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R.oo" : { + "Package" : "R.oo", + "Version" : "1.25.0", + "Source" : "Repository", + "Repository" : "CRAN" + }, + "R.utils" : { + "Package" : "R.utils", + "Version" : "2.12.2", + "Source" : "Repository", + "Repository" : "CRAN" + }, "renv" : { "Package" : "renv", - "Version" : "0.17.2", + "Version" : "1.0.3", "Source" : "Repository", "Repository" : "CRAN" }, "CirceR" : { "Package" : "CirceR", - "Version" : "1.3.0", + "Version" : "1.3.1", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "CirceR", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v1.3.0" + "RemoteRef" : "v1.3.1" }, "FeatureExtraction" : { "Package" : "FeatureExtraction", - "Version" : "3.2.0", + "Version" : "3.3.1", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "FeatureExtraction", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v3.2.0" + "RemoteRef" : "v3.3.1" }, "CohortGenerator" : { "Package" : "CohortGenerator", @@ -1245,23 +1353,23 @@ }, "PatientLevelPrediction" : { "Package" : "PatientLevelPrediction", - "Version" : "6.3.1", + "Version" : "6.3.5", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "PatientLevelPrediction", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v6.3.1" + "RemoteRef" : "v6.3.5" }, "ResultModelManager" : { "Package" : "ResultModelManager", - "Version" : "0.3.0", + "Version" : "0.5.1", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "ResultModelManager", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v0.3.0" + "RemoteRef" : "v0.5.1" }, "BigKnn" : { "Package" : "BigKnn", @@ -1275,13 +1383,13 @@ }, "Capr" : { "Package" : "Capr", - "Version" : "2.0.0", + "Version" : "2.0.7", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "Capr", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v2.0.0" + "RemoteRef" : "v2.0.7" }, "Characterization" : { "Package" : "Characterization", @@ -1295,53 +1403,43 @@ }, "CohortDiagnostics" : { "Package" : "CohortDiagnostics", - "Version" : "3.1.2", + "Version" : "3.2.4", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "CohortDiagnostics", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v3.1.2" - }, - "CohortExplorer" : { - "Package" : "CohortExplorer", - "Version" : "0.0.11", - "Source" : "GitHub", - "RemoteType" : "github", - "RemoteHost" : "api.github.com", - "RemoteRepo" : "CohortExplorer", - "RemoteUsername" : "ohdsi", - "RemoteRef" : "v0.0.11" + "RemoteRef" : "v3.2.4" }, "CohortMethod" : { "Package" : "CohortMethod", - "Version" : "4.2.3", + "Version" : "5.1.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "CohortMethod", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v4.2.3" + "RemoteRef" : "v5.1.0" }, "DataQualityDashboard" : { "Package" : "DataQualityDashboard", - "Version" : "2.1.2", + "Version" : "2.4.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "DataQualityDashboard", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v2.1.2" + "RemoteRef" : "v2.4.0" }, "DeepPatientLevelPrediction" : { "Package" : "DeepPatientLevelPrediction", - "Version" : "1.1.2", + "Version" : "2.0.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "DeepPatientLevelPrediction", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v1.1.2" + "RemoteRef" : "v2.0.0" }, "EnsemblePatientLevelPrediction" : { "Package" : "EnsemblePatientLevelPrediction", @@ -1375,13 +1473,13 @@ }, "MethodEvaluation" : { "Package" : "MethodEvaluation", - "Version" : "2.2.0", + "Version" : "2.3.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "MethodEvaluation", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v2.2.0" + "RemoteRef" : "v2.3.0" }, "OhdsiSharing" : { "Package" : "OhdsiSharing", @@ -1395,23 +1493,23 @@ }, "PhenotypeLibrary" : { "Package" : "PhenotypeLibrary", - "Version" : "3.12.0", + "Version" : "3.25.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "PhenotypeLibrary", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v3.12.0" + "RemoteRef" : "v3.25.0" }, "PheValuator" : { "Package" : "PheValuator", - "Version" : "2.2.2", + "Version" : "2.2.10", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "PheValuator", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v2.2.2" + "RemoteRef" : "v2.2.10" }, "ROhdsiWebApi" : { "Package" : "ROhdsiWebApi", @@ -1425,13 +1523,13 @@ }, "SelfControlledCaseSeries" : { "Package" : "SelfControlledCaseSeries", - "Version" : "4.1.0", + "Version" : "4.2.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "SelfControlledCaseSeries", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v4.1.0" + "RemoteRef" : "v4.2.0" }, "SelfControlledCohort" : { "Package" : "SelfControlledCohort", @@ -1445,23 +1543,23 @@ }, "ShinyAppBuilder" : { "Package" : "ShinyAppBuilder", - "Version" : "1.1.1", + "Version" : "1.1.2", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "ShinyAppBuilder", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v1.1.1" + "RemoteRef" : "v1.1.2" }, "Hades" : { "Package" : "Hades", - "Version" : "1.11.0", + "Version" : "1.13.0", "Source" : "GitHub", "RemoteType" : "github", "RemoteHost" : "api.github.com", "RemoteRepo" : "Hades", "RemoteUsername" : "ohdsi", - "RemoteRef" : "v1.11.0" + "RemoteRef" : "v1.13.0" } } }