From 699356160215d21965f28ad9a5982313800e7a7a Mon Sep 17 00:00:00 2001
From: Ger Inberg Schuemie M, Suchard M, Ryan P, Reps J, Sena A, Inberg G (2025).
FeatureExtraction: Generating Features for a Cohort.
-R package version 3.10.0, https://github.com/OHDSI/FeatureExtraction.
+R package version 3.11.0, https://github.com/OHDSI/FeatureExtraction.
Creating covariates based on other cohorts
Martijn J.
Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/CreatingCovariatesBasedOnOtherCohorts.Rmd
CreatingCovariatesBasedOnOtherCohorts.RmdCreating covariates using cohort attributes
Martijn J.
Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/CreatingCovariatesUsingCohortAttributes.Rmd
CreatingCovariatesUsingCohortAttributes.RmdCreating custom covariate builders
Martijn J.
Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/CreatingCustomCovariateBuilders.Rmd
CreatingCustomCovariateBuilders.RmdCreating custom covariate builders (Korean)
Jeon Ga Bin
& Martijn J. Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/CreatingCustomCovariateBuildersKorean.Rmd
CreatingCustomCovariateBuildersKorean.RmdUsing FeatureExtraction
Martijn J.
Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/UsingFeatureExtraction.Rmd
UsingFeatureExtraction.RmdUsing FeatureExtraction (Korean)
Jeon Ga Bin
& Martijn J. Schuemie
- 2025-05-08
+ 2025-09-01
Source: vignettes/UsingFeatureExtractionKorean.Rmd
UsingFeatureExtractionKorean.RmdCitation
@Manual{,
title = {FeatureExtraction: Generating Features for a Cohort},
author = {Martijn Schuemie and Marc Suchard and Patrick Ryan and Jenna Reps and Anthony Sena and Ger Inberg},
year = {2025},
- note = {R package version 3.10.0},
+ note = {R package version 3.11.0},
url = {https://github.com/OHDSI/FeatureExtraction},
}
diff --git a/docs/index.html b/docs/index.html
index 8bcac0df..3a0e982a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -33,7 +33,7 @@
diff --git a/docs/news/index.html b/docs/news/index.html
index 50c8b3d3..9b302eb3 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
@@ -76,7 +76,7 @@ Changelog
FeatureExtraction 3.10.0
+FeatureExtraction 3.10.02025-05-08
Examples
temporal = FALSE
)
aggregatedCovariateData <- aggregateCovariates(covariateData)
-#> Aggregating covariates took 0.406 secs
+#> Aggregating covariates took 0.53 secs
# }
diff --git a/docs/reference/computeStandardizedDifference.html b/docs/reference/computeStandardizedDifference.html
index 2ca0ea04..3d750b94 100644
--- a/docs/reference/computeStandardizedDifference.html
+++ b/docs/reference/computeStandardizedDifference.html
@@ -18,7 +18,7 @@
@@ -123,7 +123,8 @@ Value
Examples
# \donttest{
binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
- package = "FeatureExtraction")
+ package = "FeatureExtraction"
+)
covariateData1 <- loadCovariateData(binaryCovDataFile)
covariateData2 <- loadCovariateData(binaryCovDataFile)
covDataDiff <- computeStandardizedDifference(
diff --git a/docs/reference/convertPrespecSettingsToDetailedSettings.html b/docs/reference/convertPrespecSettingsToDetailedSettings.html
index e6100edb..8986e829 100644
--- a/docs/reference/convertPrespecSettingsToDetailedSettings.html
+++ b/docs/reference/convertPrespecSettingsToDetailedSettings.html
@@ -17,7 +17,7 @@
Examples
#> Connecting using SQLite driver
#> Constructing features on server
#>
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-#> Executing SQL took 1.05 secs
+#> Executing SQL took 1.11 secs
#> Fetching data from server
-#> Fetching data took 0.0951 secs
+#> Fetching data took 0.236 secs
covData2 <- getDbCovariateData(
connectionDetails = eunomiaConnectionDetails,
tempEmulationSchema = NULL,
@@ -219,9 +219,9 @@ Examples
#> Connecting using SQLite driver
#> Constructing features on server
#>
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-#> Executing SQL took 0.831 secs
+#> Executing SQL took 0.905 secs
#> Fetching data from server
-#> Fetching data took 0.0914 secs
+#> Fetching data took 0.3 secs
table1 <- createTable1(
covariateData1 = covData1,
covariateData2 = covData2,
diff --git a/docs/reference/createTable1CovariateSettings.html b/docs/reference/createTable1CovariateSettings.html
index 3d6d1eff..d0e9ee65 100644
--- a/docs/reference/createTable1CovariateSettings.html
+++ b/docs/reference/createTable1CovariateSettings.html
@@ -19,7 +19,7 @@
diff --git a/docs/reference/createTemporalCovariateSettings.html b/docs/reference/createTemporalCovariateSettings.html
index b91713e3..f6d4fab7 100644
--- a/docs/reference/createTemporalCovariateSettings.html
+++ b/docs/reference/createTemporalCovariateSettings.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/createTemporalSequenceCovariateSettings.html b/docs/reference/createTemporalSequenceCovariateSettings.html
index 31953d2d..d47b091e 100644
--- a/docs/reference/createTemporalSequenceCovariateSettings.html
+++ b/docs/reference/createTemporalSequenceCovariateSettings.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/dot-createLooCovariateSettings.html b/docs/reference/dot-createLooCovariateSettings.html
index 152df9fb..0b718d6e 100644
--- a/docs/reference/dot-createLooCovariateSettings.html
+++ b/docs/reference/dot-createLooCovariateSettings.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/dot-getDbLooCovariateData.html b/docs/reference/dot-getDbLooCovariateData.html
index 8a461949..0a6bfced 100644
--- a/docs/reference/dot-getDbLooCovariateData.html
+++ b/docs/reference/dot-getDbLooCovariateData.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/filterByCohortDefinitionId.html b/docs/reference/filterByCohortDefinitionId.html
index 202f7781..e5ea4c89 100644
--- a/docs/reference/filterByCohortDefinitionId.html
+++ b/docs/reference/filterByCohortDefinitionId.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/filterByRowId.html b/docs/reference/filterByRowId.html
index 60919c92..9c8092e7 100644
--- a/docs/reference/filterByRowId.html
+++ b/docs/reference/filterByRowId.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/getDbCohortAttrCovariatesData.html b/docs/reference/getDbCohortAttrCovariatesData.html
index 415d9e6d..a09966d5 100644
--- a/docs/reference/getDbCohortAttrCovariatesData.html
+++ b/docs/reference/getDbCohortAttrCovariatesData.html
@@ -17,7 +17,7 @@
@@ -237,8 +237,8 @@ Examples
aggregated = FALSE
)
#> Constructing covariates from cohort attributes table
-#> Inserting data took 0.00612 secs
-#> Loading took 0.0243 secs
+#> Inserting data took 0.00668 secs
+#> Loading took 0.0282 secs
# }
diff --git a/docs/reference/getDbCohortBasedCovariatesData.html b/docs/reference/getDbCohortBasedCovariatesData.html
index f197f1cd..228eb5d3 100644
--- a/docs/reference/getDbCohortBasedCovariatesData.html
+++ b/docs/reference/getDbCohortBasedCovariatesData.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/getDbCovariateData.html b/docs/reference/getDbCovariateData.html
index 559bab4d..26e1546f 100644
--- a/docs/reference/getDbCovariateData.html
+++ b/docs/reference/getDbCovariateData.html
@@ -17,7 +17,7 @@
@@ -96,7 +96,9 @@ Get covariate information from the database
covariateSettings,
aggregated = FALSE,
minCharacterizationMean = 0,
- tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
+ tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
+ covariateCohortDatabaseSchema = NULL,
+ covariateCohortTable = NULL
)
@@ -192,6 +194,14 @@ Arguments
temp tables. To emulate temp tables, provide a schema with write
privileges where temp tables can be created.
The database schema where the cohorts used to define the covariates can be found.
The table where the cohorts used to define the covariates can be found.
loadCovariateData()
Load the covariate data from a folder
Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings
# \donttest{
binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
- package = "FeatureExtraction")
+ package = "FeatureExtraction"
+)
covData <- loadCovariateData(binaryCovDataFile)
isCovData <- isCovariateData(covData)
# }
diff --git a/docs/reference/isTemporalCovariateData.html b/docs/reference/isTemporalCovariateData.html
index 59c5a618..311c8c9d 100644
--- a/docs/reference/isTemporalCovariateData.html
+++ b/docs/reference/isTemporalCovariateData.html
@@ -17,7 +17,7 @@
# \donttest{
binaryCovDataFile <- system.file("testdata/binaryCovariateData.zip",
- package = "FeatureExtraction")
+ package = "FeatureExtraction"
+)
covData <- loadCovariateData(binaryCovDataFile)
# }
diff --git a/docs/reference/replaceCovariateSettingsCohortSchemaTable.html b/docs/reference/replaceCovariateSettingsCohortSchemaTable.html
new file mode 100644
index 00000000..f978a3f6
--- /dev/null
+++ b/docs/reference/replaceCovariateSettingsCohortSchemaTable.html
@@ -0,0 +1,137 @@
+
+Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings — replaceCovariateSettingsCohortSchemaTable • FeatureExtraction
+
+
+
+
+
+
+
+
+
+
+ Utility function to set the cohort table & schema on createCohortBasedCovariateSettings with information from the execution settings
+ Source: R/GetCovariatesFromOtherCohorts.R
+ replaceCovariateSettingsCohortSchemaTable.Rd
+
+
+
+ Utility function to set the cohort table & schema on createCohortBasedCovariateSettings
+with information from the execution settings
+
+
+
+ replaceCovariateSettingsCohortSchemaTable(
+ covariateSettings,
+ covariateCohortDatabaseSchema,
+ covariateCohortTable
+)
+
+
+
+ Arguments
+
+
+
+
+ Value
+ An object of type covariateSettings
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/saveCovariateData.html b/docs/reference/saveCovariateData.html
index 05594696..f2061455 100644
--- a/docs/reference/saveCovariateData.html
+++ b/docs/reference/saveCovariateData.html
@@ -17,7 +17,7 @@
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zF|gyR8A I3L?so&}kHWi-*3nta6Sjp$fbGX$Ul~=rZMJ`AzFc{rf
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z-93a?q(TcZb5Jc7a zjbl;Q7R{laB2}#O6S|e{P7OU+#z1ps^{EyZm~UeEd*e|(*;
zO`
*oBMok{riB&TUn4Q4_9_L)Et=
zt+sw^Xp#k}$C@3rmOb}aka;tR>RT)j*2$5?3M~oOFO#9zbJmwZ>bVP9GKKCMNnO{I
zNwd=VCZo08wU_6i>BCU`_1jvlE*;~4HEF$763Cq=PvUSX@*)-dudJU7Rx?S}u7^rT
zauhUnV|cPdS^$IL9jh&}bHDhj@K{LFGK!clvDSaIETg26@&v_LqqHRk6AFR6M0&o3
zF~wWNUrT1Lgcm4|&i2&XqtexTN*`wl><1qJcQY(0F^JdxI1f#Jfi{)kVcfkW`K=I?(v?78P33o^rx3o
zQV+|2i)yE`xMmPtl)Ztm-#Tg;uNDu*9