diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml index 0ba1cc92..db1df5be 100644 --- a/.github/workflows/R_CMD_check_Hades.yaml +++ b/.github/workflows/R_CMD_check_Hades.yaml @@ -24,7 +24,7 @@ jobs: - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"} - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"} - - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"} + #- {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"} - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: diff --git a/DESCRIPTION b/DESCRIPTION index a19bfc14..e0fc6cf3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: Strategus Type: Package Title: Coordinating and Executing Analytics Using HADES Modules Version: 0.1.0 -Date: 2023-09-25 +Date: 2023-10-04 Authors@R: c( person("Martijn", "Schuemie", email = "schuemie@ohdsi.org", role = c("aut")), person("Anthony", "Sena", email = "sena@ohdsi.org", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index 9f6b07b1..1fd7ea44 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,19 @@ +Strategus 0.1.0 +=============== + +- Adds an initial implementation for uploading results to a results database (#72) +- Robust handling of connection details via keyring (#74) +- Ensures uniqueness of all CDM tables when gathering database metadata (#82) +- `tempEmulationSchema` added to execution settings and passed properly to modules (#82) +- Adding logging to module initalization to detect `renv` restore errors (#82) +- Adopt HADES-wide lock file in latest versions of all modules (#83) +- Use renv >= v1.0.0 for all modules and Strategus (#83) +- Add GitHub unit tests for HADES adopted version (currently v4.2.3) and the latest R versions for all modules and Strategus. (#83) +- Ensure all Strategus GitHub unit tests run on all operating systems and available OHDSI test database platforms (#83) +- Use CDM v5.4 schemas for all unit tests (#85) +- Allow for passing `renv`configuration options when running Strategus (#88) +- Adds SQL for test cohorts to package (#1) + Strategus 0.0.6 =============== diff --git a/docs/articles/CreatingAnalysisSpecification.html b/docs/articles/CreatingAnalysisSpecification.html index db88e049..f2e5a14d 100644 --- a/docs/articles/CreatingAnalysisSpecification.html +++ b/docs/articles/CreatingAnalysisSpecification.html @@ -94,7 +94,7 @@
vignettes/CreatingAnalysisSpecification.Rmd
CreatingAnalysisSpecification.Rmd
kable(cohortDefinitionSet[, c("cohortId", "cohortName")])
cohortId | -cohortName | -
---|---|
1 | -Celecoxib | -
2 | -Diclofenac | -
3 | -GI bleed | -
4 | -Celecoxib age 30 or older | -
5 | -Diclofenac age 30 or older | -
And the negative control outcomes when performing empirical calibration.
kable(ncoCohortSet)
cohortId | -cohortName | -outcomeConceptId | -
---|---|---|
1001 | -Acute pancreatitis | -199074 | -
1002 | -Alcohol abuse | -433753 | -
1003 | -Allergic rhinitis | -257007 | -
1004 | -Amenorrhea | -443800 | -
1005 | -Bipolar disorder | -436665 | -
1006 | -Candida infection of genital region | -4084966 | -
1007 | -Candidiasis of mouth | -29735 | -
1008 | -Cardiomegaly | -314658 | -
1009 | -Carotid artery obstruction | -4288310 | -
1010 | -Carpal tunnel syndrome | -380094 | -
1011 | -Chronic obstructive lung disease | -255573 | -
1012 | -Conduct disorder | -443617 | -
1013 | -Dysplasia of cervix | -192367 | -
1014 | -Gastrointestinal hemorrhage | -192671 | -
1015 | -Hirsutism | -134718 | -
1016 | -Hydronephrosis | -433811 | -
1017 | -Hypersomnia | -438134 | -
1018 | -Hypoglycemia | -24609 | -
1019 | -Infectious mononucleosis | -437784 | -
1020 | -Ingrowing nail | -139099 | -
1021 | -Injury of hand | -80004 | -
1022 | -Lipoma (clinical) | -440358 | -
1023 | -Lymphadenitis | -316084 | -
1024 | -Metabolic syndrome X | -436940 | -
1025 | -Mitral valve disorder | -319843 | -
1026 | -Obsessive-compulsive disorder | -440374 | -
1027 | -Ovarian failure | -193739 | -
1028 | -Perforation of tympanic membrane | -375292 | -
1029 | -Peripheral venous insufficiency | -321596 | -
1030 | -Posttraumatic stress disorder | -436676 | -
1031 | -Prostatitis | -194997 | -
1032 | -Restless legs | -73754 | -
1033 | -Senile hyperkeratosis | -141932 | -
1034 | -Sensorineural hearing loss | -374366 | -
1035 | -Sleep apnea | -313459 | -
1036 | -Uterine leiomyoma | -197236 | -
vignettes/CreatingModules.Rmd
CreatingModules.Rmd
vignettes/ExecuteStrategus.Rmd
ExecuteStrategus.Rmd
vignettes/IntroductionToStrategus.Rmd
IntroductionToStrategus.Rmd
Strategus is an R package for coordinating and executing analytics using HADES modules.
+Strategus is an R package for coordinating and executing analytics using HADES modules. Please see the Introduction To Strategus for more details.
install.packages("remotes")
remotes::install_github("ohdsi/Strategus")
Run in a terminal the following before installing keyring:
+sudo yum install libsodium libsodium-devel
+sudo yum install libsecret libsecret-devel
+sudo chmod 777 /home/idies/.config
NEWS.md
tempEmulationSchema
added to execution settings and passed properly to modules (#82)renv
restore errors (#82)renv
configuration options when running Strategus (#88)inst/testdata/analysisSpecification.json
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f04c235d..6cfb522f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
CreatingModules: CreatingModules.html
ExecuteStrategus: ExecuteStrategus.html
IntroductionToStrategus: IntroductionToStrategus.html
-last_built: 2023-09-25T22:09Z
+last_built: 2023-10-04T19:26Z
diff --git a/docs/reference/Strategus-package.html b/docs/reference/Strategus-package.html
index ebde69fb..956bac9e 100644
--- a/docs/reference/Strategus-package.html
+++ b/docs/reference/Strategus-package.html
@@ -84,8 +84,8 @@