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" : "4.2.3",
+ "Repositories" : [
+ {
+ "Name" : "CRAN",
+ "URL" : "https://cloud.r-project.org"
+ }
+ ]
+ },
+ "Packages" : {
+ "cli" : {
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+ "Repository" : "CRAN"
+ },
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+ "rlang" : {
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+ "R6" : {
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+ "utf8" : {
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+ "vctrs" : {
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+ "Repository" : "CRAN"
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+ "ellipsis" : {
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+}
diff --git a/hadesWideReleases/2023Q1/README.md b/hadesWideReleases/2023Q1/README.md
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 @@
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+ "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"
}
}
}