CirceR, Eunomia, and FeatureExtraction now in CRAN. Updating Java ins…

…tallation instructions.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Hades
 Type: Package
 Title: Health Analytics Data-to-Evidence Suite
-Version: 1.13.0
-Date: 2023-05-19
+Version: 1.13.1
+Date: 2024-05-08
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
   person("Observational Health Data Science and Informatics", role = c("cph"))
@@ -52,7 +52,6 @@ Remotes:
   ohdsi/BigKnn,
   ohdsi/ROhdsiWebApi,
   ohdsi/EnsemblePatientLevelPrediction,
-  ohdsi/FeatureExtraction,
   ohdsi/CohortDiagnostics,
   ohdsi/CohortMethod,
   ohdsi/SelfControlledCaseSeries,
@@ -63,9 +62,7 @@ Remotes:
   ohdsi/PhenotypeLibrary,
   ohdsi/PheValuator,
   ohdsi/Hydra,
-  ohdsi/CirceR,
   ohdsi/Capr,
-  ohdsi/Eunomia,
   ohdsi/CohortGenerator,
   ohdsi/DeepPatientLevelPrediction,
   ohdsi/CohortExplorer,

NEWS.md

@@ -1,3 +1,8 @@
+HADES 1.13.1
+============
+
+- CirceR, Eunomia, and FeatureExtraction are now in CRAN. Removing reference to Github repos.
+
 HADES 1.13.0
 ============
 

Rmd/rSetup.Rmd

@@ -62,7 +62,7 @@ rToolsUrl <- sprintf("https://cran.r-project.org/bin/windows/Rtools/rtools%s/rto
 
 ## Installing Java
 
-1.  Go to <https://docs.aws.amazon.com/corretto/latest/corretto-8-ug/downloads-list.html>, and select the Windows 64-bit JRE installer as highlighted below. ![](images/downloadJavaWindows.png)
+1.  Go to <https://docs.aws.amazon.com/corretto/latest/corretto-8-ug/downloads-list.html>, and select the Windows 64-bit JDK installer as highlighted below. ![](images/downloadJavaWindows.png)
 
 2.  After downloading just run the installer.
 

Rmd/validation.Rmd

@@ -8,7 +8,10 @@ output:
 
 # Validation
 
-Coming soon...
+For validation, HADES mostly relies on an extensive set of unit tests executed as part of its continuous integration. This assures validity on a continuous basis, at every release. A good reference would be our recent HADES paper:
+
+- Schuemie M, Reps J, Black A, et al. [Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research](https://ebooks.iospress.nl/doi/10.3233/SHTI231108) Studies in health technology and informatics. 2024 Jan 25:310:966-970. 
+
 
 # Evaluation
 

docs/packageStatuses.html

@@ -578,7 +578,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
 src="https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20"
 alt="Version" /></a></td>
 <td align="left">Chris Knoll</td>
-<td align="center">GitHub</td>
+<td align="center">CRAN</td>
 <td align="center"><a href="https://github.com/OHDSI/CirceR/issues"><img
 src="https://img.shields.io/github/issues-raw/OHDSI/CirceR?label=%20"
 alt="Open issues" /></a></td>
@@ -878,7 +878,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
 src="https://img.shields.io/github/r-package/v/ohdsi/Eunomia?label=%20"
 alt="Version" /></a></td>
 <td align="left">Frank DeFalco</td>
-<td align="center">GitHub</td>
+<td align="center">CRAN</td>
 <td align="center"><a
 href="https://github.com/OHDSI/Eunomia/issues"><img
 src="https://img.shields.io/github/issues-raw/OHDSI/Eunomia?label=%20"
@@ -931,8 +931,8 @@ <h1 class="title toc-ignore">Package statuses</h1>
 href="https://ohdsi.github.io/FeatureExtraction/"><img
 src="https://img.shields.io/github/r-package/v/ohdsi/FeatureExtraction?label=%20"
 alt="Version" /></a></td>
-<td align="left">Anthony Sena</td>
-<td align="center">GitHub</td>
+<td align="left">Ger Inberg</td>
+<td align="center">CRAN</td>
 <td align="center"><a
 href="https://github.com/OHDSI/FeatureExtraction/issues"><img
 src="https://img.shields.io/github/issues-raw/OHDSI/FeatureExtraction?label=%20"

docs/rSetup.html

@@ -523,7 +523,7 @@ <h2>Installing Java</h2>
 <li><p>Go to <a
 href="https://docs.aws.amazon.com/corretto/latest/corretto-8-ug/downloads-list.html"
 class="uri">https://docs.aws.amazon.com/corretto/latest/corretto-8-ug/downloads-list.html</a>,
-and select the Windows 64-bit JRE installer as highlighted below. <img
+and select the Windows 64-bit JDK installer as highlighted below. <img
 src="images/downloadJavaWindows.png" /></p></li>
 <li><p>After downloading just run the installer.</p></li>
 <li><p>The default maximum Java heap space is very small (only 512MB),

docs/validation.html

@@ -446,7 +446,17 @@ <h1 class="title toc-ignore">Validation &amp; Evaluation</h1>
 
 <div id="validation" class="section level1">
 <h1>Validation</h1>
-<p>Coming soon…</p>
+<p>For validation, HADES mostly relies on an extensive set of unit tests
+executed as part of its continuous integration. This assures validity on
+a continuous basis, at every release. A good reference would be our
+recent HADES paper:</p>
+<ul>
+<li>Schuemie M, Reps J, Black A, et al. <a
+href="https://ebooks.iospress.nl/doi/10.3233/SHTI231108">Health-Analytics
+Data to Evidence Suite (HADES): Open-Source Software for Observational
+Research</a> Studies in health technology and informatics. 2024 Jan
+25:310:966-970.</li>
+</ul>
 </div>
 <div id="evaluation" class="section level1">
 <h1>Evaluation</h1>

extras/GeneratePackagesPage.R

@@ -1,4 +1,4 @@
-setwd("C:/Temp/Git/Hades")
+# setwd("C:/Temp/Git/Hades")
 packages <- read.csv("extras/packages.csv", stringsAsFactors = FALSE)
 # sections <- read.csv("extras/sections.csv", stringsAsFactors = FALSE)
 

extras/packages.csv

@@ -8,7 +8,7 @@ order,name,section,description,inCran,pages,maintainers,CRON
 7,EnsemblePatientLevelPrediction,Patient-level prediction,Building and validating ensemble patient-level predictive models.,FALSE,TRUE,Jenna Reps,0 14 * * 6
 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
+10,CirceR,Cohort construction and evaluation,"An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.",TRUE,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
@@ -18,13 +18,13 @@ order,name,section,description,inCran,pages,maintainers,CRON
 17,DataQualityDashboard,Evidence Quality,Expose and evaluate observational data quality.,FALSE,TRUE,Katy Sadowksi,0 17 * * 0
 18,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie,0 22 * * 6
 19,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
-20,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
+20,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,Martijn Schuemie,0 0 * * 0
 21,BigKnn,Supporting packages,A large scale k-nearest neighbor classifier using the Lucene search engine.,FALSE,TRUE,Martijn Schuemie ,0 1 * * 0
 22,BrokenAdaptiveRidge,Supporting packages,Broken Adaptive Ridge Regression with Cyclops.,TRUE,TRUE,Marc Suchard,0 18 * * 0
 23,Cyclops,Supporting packages,"Highly efficient implementation of regularized logistic, Poisson and Cox regression.",TRUE,TRUE,Marc Suchard,0 2 * * 0
 24,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
-25,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
-26,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
+25,Eunomia,Supporting packages,A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.,TRUE,TRUE,Frank DeFalco,0 4 * * 0
+26,FeatureExtraction,Supporting packages,Automatically extract large sets of features for user-specified cohorts using data in the CDM.,TRUE,TRUE,Ger Inberg,0 5 * * 0
 27,Hydra,Supporting packages,Hydrating package skeletons into executable R study packages based on specifications in JSON format.,FALSE,TRUE,Anthony Sena ,0 6 * * 0
 28,IterativeHardThresholding,Supporting packages,Performing L0-based regressions using Cyclops,TRUE,TRUE,Marc Suchard,0 7 * * 0
 29,OhdsiSharing,Supporting packages,Securely sharing (large) files between OHDSI collaborators.,FALSE,TRUE,Lee Evans,0 8 * * 0