diff --git a/DESCRIPTION b/DESCRIPTION index 83c9403..b8e917e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: Hades Type: Package Title: Health Analytics Data-to-Evidence Suite -Version: 1.8.0 +Version: 1.9.0 Date: 2023-01-11 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), @@ -42,7 +42,8 @@ Imports: Hydra, IterativeHardThresholding, OhdsiShinyModules, - ResultModelManager + ResultModelManager, + Characterization Remotes: ohdsi/BigKnn, ohdsi/ROhdsiWebApi, @@ -65,7 +66,8 @@ Remotes: ohdsi/DeepPatientLevelPrediction, ohdsi/CohortExplorer, ohdsi/OhdsiShinyModules, - ohdsi/ResultModelManager + ohdsi/ResultModelManager, + ohdsi/Characterization LazyData: false RoxygenNote: 7.2.0 Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index 1ae2bbb..bc3bc3d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +HADES 1.9.0 +=========== + +Changes + +- Adding Characterization to HADES + HADES 1.8.0 =========== diff --git a/Rmd/packageStatuses.Rmd b/Rmd/packageStatuses.Rmd index fce6d7e..9f4e23f 100644 --- a/Rmd/packageStatuses.Rmd +++ b/Rmd/packageStatuses.Rmd @@ -21,6 +21,7 @@ The table below lists, for each of the HADES packages, the following details: | [Andromeda](https://github.com/OHDSI/Andromeda) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Andromeda?label=%20)](https://ohdsi.github.io/Andromeda/) | Adam Black | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Andromeda?label=%20)](https://github.com/OHDSI/Andromeda/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Andromeda?label=%20)](https://github.com/OHDSI/Andromeda/pulls) | [![Build Status](https://github.com/OHDSI/Andromeda/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Andromeda/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Andromeda/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Andromeda?branch=main) | | [BigKnn](https://github.com/OHDSI/BigKnn) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/BigKnn?label=%20)](https://ohdsi.github.io/BigKnn/) | Martijn Schuemie | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/BigKnn?label=%20)](https://github.com/OHDSI/BigKnn/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/BigKnn?label=%20)](https://github.com/OHDSI/BigKnn/pulls) | [![Build Status](https://github.com/OHDSI/BigKnn/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/BigKnn/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/BigKnn/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/BigKnn?branch=main) | | [Capr](https://github.com/OHDSI/Capr) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Capr?label=%20)](https://ohdsi.github.io/Capr/) | Martin Lavallee | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Capr?label=%20)](https://github.com/OHDSI/Capr/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Capr?label=%20)](https://github.com/OHDSI/Capr/pulls) | [![Build Status](https://github.com/OHDSI/Capr/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Capr/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Capr/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Capr?branch=main) | +| [Characterization](https://github.com/OHDSI/Characterization) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Characterization?label=%20)](https://ohdsi.github.io/Characterization/) | Jenna Reps | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Characterization?label=%20)](https://github.com/OHDSI/Characterization/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Characterization?label=%20)](https://github.com/OHDSI/Characterization/pulls) | [![Build Status](https://github.com/OHDSI/Characterization/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Characterization/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Characterization/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Characterization?branch=main) | | [CirceR](https://github.com/OHDSI/CirceR) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20)](https://ohdsi.github.io/CirceR/) | Chris Knoll | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/pulls) | [![Build Status](https://github.com/OHDSI/CirceR/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CirceR/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CirceR/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CirceR?branch=main) | | [CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortDiagnostics?label=%20)](https://ohdsi.github.io/CohortDiagnostics/) | Jamie Gilbert | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/pulls) | [![Build Status](https://github.com/OHDSI/CohortDiagnostics/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortDiagnostics/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CohortDiagnostics/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortDiagnostics?branch=main) | | [CohortExplorer](https://github.com/OHDSI/CohortExplorer) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortExplorer?label=%20)](https://ohdsi.github.io/CohortExplorer/) | Gowtham Rao | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortExplorer?label=%20)](https://github.com/OHDSI/CohortExplorer/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortExplorer?label=%20)](https://github.com/OHDSI/CohortExplorer/pulls) | [![Build Status](https://github.com/OHDSI/CohortExplorer/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortExplorer/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CohortExplorer/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortExplorer?branch=main) | diff --git a/Rmd/packages.Rmd b/Rmd/packages.Rmd index 2ed18f8..b6b36d6 100644 --- a/Rmd/packages.Rmd +++ b/Rmd/packages.Rmd @@ -22,6 +22,10 @@ Below are the packages included in HADES. For each package a link is provided wi
install.packages("SqlRender")
library(SqlRender)
translate("SELECT TOP 10 * FROM person;", "postgresql")
-## [1] "SELECT * FROM person LIMIT 10;"
+## [1] "SELECT * FROM person LIMIT 10;"
+## attr(,"sqlDialect")
+## [1] "postgresql"
This function uses Java, so if all goes well we know both R and Java have been installed correctly!
Another test is to see if source packages can be built. Run the following R code to install the CohortMethod
package from the OHDSI GitHub repository:
install.packages("remotes")
diff --git a/docs/support.html b/docs/support.html
index 33d4380..5dd9f1d 100644
--- a/docs/support.html
+++ b/docs/support.html
@@ -452,6 +452,7 @@ Bug reports
+
diff --git a/extras/packages.csv b/extras/packages.csv
index 4044926..063fbf1 100644
--- a/extras/packages.csv
+++ b/extras/packages.csv
@@ -6,26 +6,27 @@ order,name,section,description,inCran,pages,maintainers,CRON
5,PatientLevelPrediction,Patient-level prediction,"Build and evaluate predictive models for user-specified outcomes, using a wide array of machine learning algorithms.",FALSE,TRUE,Jenna Reps & Peter Rijnbeek,0 12 * * 6
6,DeepPatientLevelPrediction,Patient-level prediction,Performing patient level prediction using deep learning,FALSE,TRUE,Egill Fridgeirsson,0 13 * * 6
7,EnsemblePatientLevelPrediction,Patient-level prediction,Building and validating ensemble patient-level predictive models.,FALSE,TRUE,Jenna Reps,0 14 * * 6
-8,Capr,Cohort construction and evaluation,Develop and manipulate complex cohort definitions in R,FALSE,TRUE,Martin Lavallee,0 15 * * 6
-9,CirceR,Cohort construction and evaluation,"An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.",FALSE,TRUE,Chris Knoll,0 16 * * 6
-10,CohortGenerator,Cohort construction and evaluation,Instantiating cohorts in a database based on a set of cohort definitions.,FALSE,TRUE,Anthony Sena,0 17 * * 6
-11,PhenotypeLibrary,Cohort construction and evaluation,The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.,FALSE,TRUE,Gowtham Rao,0 18 * * 6
-12,CohortDiagnostics,Cohort construction and evaluation,Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.,FALSE,TRUE,Jamie Gilbert,0 19 * * 6
-13,PheValuator,Cohort construction and evaluation,"Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.",FALSE,TRUE,Joel Swerdel,0 20 * * 6
-13,CohortExplorer,Cohort construction and evaluation,Visually explore all individual-level data of patients in a cohort,FALSE,TRUE,Gowtham Rao,0 21 * * 6
-14,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie ,0 22 * * 6
-15,MethodEvaluation,Evidence Quality,Use real data and established reference sets as well as simulations injected in real data to evaluate the performance of methods.,FALSE,TRUE,Martijn Schuemie ,0 23 * * 6
-16,Andromeda,Supporting packages,"Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.",TRUE,TRUE,Adam Black,0 0 * * 0
-17,BigKnn,Supporting packages,A large scale k-nearest neighbor classifier using the Lucene search engine.,FALSE,TRUE,Martijn Schuemie ,0 1 * * 0
-18,Cyclops,Supporting packages,"Highly efficient implementation of regularized logistic, Poisson and Cox regression.",TRUE,TRUE,Marc Suchard,0 2 * * 0
-19,DatabaseConnector,Supporting packages,"Connect directly to a wide range of database platforms, including SQL Server, Oracle, and PostgreSQL.",TRUE,TRUE,Martijn Schuemie ,0 3 * * 0
-20,Eunomia,Supporting packages,A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.,FALSE,TRUE,Frank DeFalco,0 4 * * 0
-21,FeatureExtraction,Supporting packages,Automatically extract large sets of features for user-specified cohorts using data in the CDM.,FALSE,TRUE,Anthony Sena,0 5 * * 0
-22,Hydra,Supporting packages,Hydrating package skeletons into executable R study packages based on specifications in JSON format.,FALSE,TRUE,Anthony Sena ,0 6 * * 0
-23,IterativeHardThresholding,Supporting packages,Performing L0-based regressions using Cyclops,TRUE,TRUE,Marc Suchard,0 7 * * 0
-24,OhdsiSharing,Supporting packages,Securely sharing (large) files between OHDSI collaborators.,FALSE,TRUE,Lee Evans,0 8 * * 0
-25,OhdsiShinyModules,Supporting packages,Contains shiny modules that can be used within shiny result interfaces,FALSE,TRUE,Jenna Reps,0 9 * * 0
-25,ParallelLogger,Supporting packages,"Support for parallel computation with logging to console, disk, or e-mail.",TRUE,TRUE,Martijn Schuemie ,0 10 * * 0
-26,ResultModelManager,Supporting packages,"A lightweight utility for data migrations allowing old results to work with new shiny apps and data visualisations.",FALSE,TRUE,Jamie Gilbert,0 13 * * 0
-27,ROhdsiWebApi,Supporting packages,Interact with OHDSI WebAPI web services.,FALSE,TRUE,Gowtham Rao,0 11 * * 0
-28,SqlRender,Supporting packages,Generate SQL on the fly for the various SQL dialects.,TRUE,TRUE,Martijn Schuemie ,0 12 * * 0
+8,Characterization,Characterization,Various types of characterizations of a target and outcome cohort.,FALSE,TRUE,Jenna Reps,0 14 * * 0
+9,Capr,Cohort construction and evaluation,Develop and manipulate complex cohort definitions in R,FALSE,TRUE,Martin Lavallee,0 15 * * 6
+10,CirceR,Cohort construction and evaluation,"An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.",FALSE,TRUE,Chris Knoll,0 16 * * 6
+11,CohortGenerator,Cohort construction and evaluation,Instantiating cohorts in a database based on a set of cohort definitions.,FALSE,TRUE,Anthony Sena,0 17 * * 6
+12,PhenotypeLibrary,Cohort construction and evaluation,The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.,FALSE,TRUE,Gowtham Rao,0 18 * * 6
+13,CohortDiagnostics,Cohort construction and evaluation,Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.,FALSE,TRUE,Jamie Gilbert,0 19 * * 6
+14,PheValuator,Cohort construction and evaluation,"Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.",FALSE,TRUE,Joel Swerdel,0 20 * * 6
+15,CohortExplorer,Cohort construction and evaluation,Visually explore all individual-level data of patients in a cohort,FALSE,TRUE,Gowtham Rao,0 21 * * 6
+16,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie ,0 22 * * 6
+17,MethodEvaluation,Evidence Quality,Use real data and established reference sets as well as simulations injected in real data to evaluate the performance of methods.,FALSE,TRUE,Martijn Schuemie ,0 23 * * 6
+18,Andromeda,Supporting packages,"Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.",TRUE,TRUE,Adam Black,0 0 * * 0
+19,BigKnn,Supporting packages,A large scale k-nearest neighbor classifier using the Lucene search engine.,FALSE,TRUE,Martijn Schuemie ,0 1 * * 0
+20,Cyclops,Supporting packages,"Highly efficient implementation of regularized logistic, Poisson and Cox regression.",TRUE,TRUE,Marc Suchard,0 2 * * 0
+21,DatabaseConnector,Supporting packages,"Connect directly to a wide range of database platforms, including SQL Server, Oracle, and PostgreSQL.",TRUE,TRUE,Martijn Schuemie ,0 3 * * 0
+22,Eunomia,Supporting packages,A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.,FALSE,TRUE,Frank DeFalco,0 4 * * 0
+23,FeatureExtraction,Supporting packages,Automatically extract large sets of features for user-specified cohorts using data in the CDM.,FALSE,TRUE,Anthony Sena,0 5 * * 0
+24,Hydra,Supporting packages,Hydrating package skeletons into executable R study packages based on specifications in JSON format.,FALSE,TRUE,Anthony Sena ,0 6 * * 0
+25,IterativeHardThresholding,Supporting packages,Performing L0-based regressions using Cyclops,TRUE,TRUE,Marc Suchard,0 7 * * 0
+26,OhdsiSharing,Supporting packages,Securely sharing (large) files between OHDSI collaborators.,FALSE,TRUE,Lee Evans,0 8 * * 0
+27,OhdsiShinyModules,Supporting packages,Contains shiny modules that can be used within shiny result interfaces,FALSE,TRUE,Jenna Reps,0 9 * * 0
+28,ParallelLogger,Supporting packages,"Support for parallel computation with logging to console, disk, or e-mail.",TRUE,TRUE,Martijn Schuemie ,0 10 * * 0
+29,ResultModelManager,Supporting packages,A lightweight utility for data migrations allowing old results to work with new shiny apps and data visualisations.,FALSE,TRUE,Jamie Gilbert,0 13 * * 0
+30,ROhdsiWebApi,Supporting packages,Interact with OHDSI WebAPI web services.,FALSE,TRUE,Gowtham Rao,0 11 * * 0
+31,SqlRender,Supporting packages,Generate SQL on the fly for the various SQL dialects.,TRUE,TRUE,Martijn Schuemie ,0 12 * * 0