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 @@

Creating Analysis Specification

Anthony G. Sena

-

2023-09-25

+

2023-10-04

Source: vignettes/CreatingAnalysisSpecification.Rmd @@ -154,227 +154,10 @@

Cohort Definitions & N the analysis specification for Strategus.

 kable(cohortDefinitionSet[, c("cohortId", "cohortName")])
- - - - - - - - - - - - - - - - - - - - - - - - - - - -
cohortIdcohortName
1Celecoxib
2Diclofenac
3GI bleed
4Celecoxib age 30 or older
5Diclofenac age 30 or older

And the negative control outcomes when performing empirical calibration.

 kable(ncoCohortSet)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cohortIdcohortNameoutcomeConceptId
1001Acute pancreatitis199074
1002Alcohol abuse433753
1003Allergic rhinitis257007
1004Amenorrhea443800
1005Bipolar disorder436665
1006Candida infection of genital region4084966
1007Candidiasis of mouth29735
1008Cardiomegaly314658
1009Carotid artery obstruction4288310
1010Carpal tunnel syndrome380094
1011Chronic obstructive lung disease255573
1012Conduct disorder443617
1013Dysplasia of cervix192367
1014Gastrointestinal hemorrhage192671
1015Hirsutism134718
1016Hydronephrosis433811
1017Hypersomnia438134
1018Hypoglycemia24609
1019Infectious mononucleosis437784
1020Ingrowing nail139099
1021Injury of hand80004
1022Lipoma (clinical)440358
1023Lymphadenitis316084
1024Metabolic syndrome X436940
1025Mitral valve disorder319843
1026Obsessive-compulsive disorder440374
1027Ovarian failure193739
1028Perforation of tympanic membrane375292
1029Peripheral venous insufficiency321596
1030Posttraumatic stress disorder436676
1031Prostatitis194997
1032Restless legs73754
1033Senile hyperkeratosis141932
1034Sensorineural hearing loss374366
1035Sleep apnea313459
1036Uterine leiomyoma197236
diff --git a/docs/articles/CreatingModules.html b/docs/articles/CreatingModules.html index 1ba95a7d..c8118ce2 100644 --- a/docs/articles/CreatingModules.html +++ b/docs/articles/CreatingModules.html @@ -94,7 +94,7 @@

Creating Strategus Modules

Anthony G. Sena

-

2023-09-25

+

2023-10-04

Source: vignettes/CreatingModules.Rmd diff --git a/docs/articles/ExecuteStrategus.html b/docs/articles/ExecuteStrategus.html index 92156d41..c4ee685d 100644 --- a/docs/articles/ExecuteStrategus.html +++ b/docs/articles/ExecuteStrategus.html @@ -94,7 +94,7 @@

Execute Strategus

Anthony G. Sena

-

2023-09-25

+

2023-10-04

Source: vignettes/ExecuteStrategus.Rmd diff --git a/docs/articles/IntroductionToStrategus.html b/docs/articles/IntroductionToStrategus.html index 5de6b29b..687ba698 100644 --- a/docs/articles/IntroductionToStrategus.html +++ b/docs/articles/IntroductionToStrategus.html @@ -94,7 +94,7 @@

Introduction to Strategus

Anthony G. Sena

-

2023-09-25

+

2023-10-04

Source: vignettes/IntroductionToStrategus.Rmd diff --git a/docs/index.html b/docs/index.html index 81b41f12..ce7fe7f4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -98,7 +98,7 @@

Introduction

-

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.

Features @@ -130,6 +130,13 @@

Installation
 install.packages("remotes")
 remotes::install_github("ohdsi/Strategus")

+
    +
  1. If using Linux, please refer to the keyring Linux secret service setup as this is required to execute studies using Strategus. In addition to those instructions, members of the OHDSI community have shared the following guidance:
  2. +
+

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 

User Documentation diff --git a/docs/news/index.html b/docs/news/index.html index dd8b10a3..656bc51f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -69,6 +69,22 @@

Changelog

Source: NEWS.md
+
+ +

Author

-

Maintainer: Martijn Schuemie schuemie@ohdsi.org

-

Authors:

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