Feature

.Rbuildignore

@@ -1,18 +1,20 @@
-^Capr\.Rproj$
-^\.Rproj\.user$
-.github
-deploy.sh
-compare_versions
-^doc$
-^Meta$
-^_pkgdown\.yml$
-^docs$
-^extras$
-^man-roxygen$
-^scratch$
-^work$
-^README\.Rmd$
-^pkgdown$
-^cran-comments\.md$
-^CRAN-SUBMISSION$
-^LICENSE\.md$
+^renv$
+^renv\.lock$
+^Capr\.Rproj$
+^\.Rproj\.user$
+.github
+deploy.sh
+compare_versions
+^doc$
+^Meta$
+^_pkgdown\.yml$
+^docs$
+^extras$
+^man-roxygen$
+^scratch$
+^work$
+^README\.Rmd$
+^pkgdown$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^LICENSE\.md$

.Rprofile

@@ -0,0 +1,14 @@
+# Force compile packages from source before installing
+options(
+  repos = c(CRAN = "https://cran.rstudio.com"),
+  install.packages.compile.from.source = TRUE,
+  pkgType = "source"
+)
+
+if (any(list.files() == "renv")) {
+  source("renv/activate.R")
+} else {
+  message("No renv initialized, calling renv::init()")
+  message("Please select to use only the DESCRIPTION file for dependency discovery if prompted, and next select 'Restore the project from the lockfile'")
+  renv::init()
+}

.gitignore

@@ -1,9 +1,33 @@
-.Rhistory
-.Rproj.user
-.DS_Store
-errorReportSql.txt
-*.log
-/Meta/
-work/*
-scratch/
-inst/doc
+!.gitignore
+
+# Capr
+.Rhistory
+.Rproj.user
+.DS_Store
+errorReportSql.txt
+*.log
+/Meta/
+work/*
+scratch/
+inst/doc
+
+# project-specific
+inst/config/*
+!inst/config/*-sample.yml
+
+inst/extdata/**/*
+
+!inst/extdata/phems_variable_list
+
+!inst/extdata/json
+inst/extdata/json/*
+
+!inst/extdata/standard_concepts
+inst/extdata/standard_concepts/*
+
+!inst/extdata/vocabularies
+inst/extdata/vocabularies/*
+
+!*.gitkeep
+
+renv

Capr.Rproj → Capr-PHEMS.Rproj

@@ -1,21 +1,17 @@
-Version: 1.0
-
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

DESCRIPTION

@@ -1,22 +1,24 @@
-Package: Capr
-Title: Cohort Definition Application Programming
+Package: Capr-PHEMS
+Title: Cohort Definition Application Programming - project specific for PHEMS
 Version: 2.0.8
 Authors@R: c(
     person("Martin", "Lavallee", , "martin.lavallee@boehringer-ingelheim.com", role = c("aut", "cre")),
-    person("Adam", "Black", , "black@ohdsi.org", role = c("aut"))
+    person("Adam", "Black", , "black@ohdsi.org", role = c("aut")),
+    person("Guus", "Wilmink", , "guus@thehyve.nl", role = c("aut"))
   )
 Description: Provides a programming language for defining cohort definitions in R to use in studies for Observational 
     Health Data Sciences and Informatics (OHDSI). The functions in 'Capr' allow for the programmatic creation of 
     OHDSI concept sets and cohorts that can be serialized to 'OHDSI' compatible 'json' files or to 'OHDSI-SQL'. 
     'Capr' functions can be used to create, save, and load component parts to a cohort definition allowing 
     R programmers to easily reuse cohort logic. 'Capr' provides tools to create a large number of OHDSI cohorts 
     while also helping bridge the gap between human readable descriptions of clinical phenotypes
-    and their computational implementation. 
+    and their computational implementation.
+    For PHEMS this package has been extended with additional functions to support PHEMS cohort creation. 
 License: Apache License (>= 2)
 URL: https://ohdsi.github.io/Capr/, https://github.com/OHDSI/Capr/
 BugReports: https://github.com/OHDSI/Capr/issues/
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
   R (>= 3.5.0)
 Imports: 
@@ -40,7 +42,11 @@ Imports:
     DatabaseConnector,
     SqlRender,
     generics,
-    CirceR
+    CirceR,
+    codetools,
+    readr,
+    dplyr,
+    DBI
 Suggests:
     testthat (>= 3.0.0),
     knitr,
@@ -61,4 +67,9 @@ Collate:
     'exit.R'
     'cohort.R'
     'collectCodesetId.R'
+    'conceptSets.R'
+    'countOccurrences.R'
+    'isStandard.R'
+    'isStandardCS.R'
+    'table_linked_to_concept_field.R'
     'utils.R'

NAMESPACE

@@ -1,86 +1,100 @@
-# Generated by roxygen2: do not edit by hand
-
-S3method(compile,Cohort)
-export("%>%")
-export(age)
-export(as.json)
-export(atLeast)
-export(atMost)
-export(attrition)
-export(bt)
-export(censoringEvents)
-export(cohort)
-export(compile)
-export(conditionEra)
-export(conditionOccurrence)
-export(conditionType)
-export(continuousObservation)
-export(cs)
-export(dateAdjustment)
-export(daysOfSupply)
-export(death)
-export(descendants)
-export(deviceExposure)
-export(drugEra)
-export(drugExit)
-export(drugExposure)
-export(drugQuantity)
-export(drugRefills)
-export(drugType)
-export(duringInterval)
-export(endDate)
-export(entry)
-export(eq)
-export(era)
-export(eventEnds)
-export(eventStarts)
-export(exactly)
-export(exclude)
-export(exit)
-export(female)
-export(firstOccurrence)
-export(fixedExit)
-export(getConceptSetDetails)
-export(gt)
-export(gte)
-export(lt)
-export(lte)
-export(makeCohortSet)
-export(male)
-export(mapped)
-export(measurement)
-export(measurementType)
-export(nbt)
-export(nestedWithAll)
-export(nestedWithAny)
-export(nestedWithAtLeast)
-export(nestedWithAtMost)
-export(observation)
-export(observationExit)
-export(observationType)
-export(procedure)
-export(procedureType)
-export(rangeHigh)
-export(rangeLow)
-export(readConceptSet)
-export(startDate)
-export(toCirce)
-export(unit)
-export(valueAsNumber)
-export(visit)
-export(visitType)
-export(withAll)
-export(withAny)
-export(withAtLeast)
-export(withAtMost)
-export(writeCohort)
-export(writeConceptSet)
-exportMethods("==")
-exportMethods(compile)
-import(dplyr)
-importFrom(generics,compile)
-importFrom(magrittr,"%>%")
-importFrom(methods,"slot<-")
-importFrom(rlang,"%||%")
-importFrom(rlang,":=")
-importFrom(rlang,.data)
+# Generated by roxygen2: do not edit by hand
+
+S3method(compile,Cohort)
+export("%>%")
+export(age)
+export(as.json)
+export(atLeast)
+export(atMost)
+export(attrition)
+export(bt)
+export(censoringEvents)
+export(cohort)
+export(compile)
+export(conceptSets)
+export(conditionEra)
+export(conditionOccurrence)
+export(conditionType)
+export(continuousObservation)
+export(countOccurrences)
+export(cs)
+export(dateAdjustment)
+export(daysOfSupply)
+export(death)
+export(descendants)
+export(deviceExposure)
+export(drugEra)
+export(drugExit)
+export(drugExposure)
+export(drugQuantity)
+export(drugRefills)
+export(drugType)
+export(duringInterval)
+export(endDate)
+export(entry)
+export(eq)
+export(era)
+export(eventEnds)
+export(eventStarts)
+export(exactly)
+export(exclude)
+export(exit)
+export(female)
+export(firstOccurrence)
+export(fixedExit)
+export(getConceptSetDetails)
+export(gt)
+export(gte)
+export(isStandard)
+export(isStandardCS)
+export(links)
+export(lt)
+export(lte)
+export(makeCohortSet)
+export(male)
+export(mapped)
+export(measurement)
+export(measurementType)
+export(nbt)
+export(nestedWithAll)
+export(nestedWithAny)
+export(nestedWithAtLeast)
+export(nestedWithAtMost)
+export(observation)
+export(observationExit)
+export(observationType)
+export(procedure)
+export(procedureType)
+export(rangeHigh)
+export(rangeLow)
+export(readConceptSet)
+export(startDate)
+export(toCirce)
+export(unit)
+export(valueAsNumber)
+export(visit)
+export(visitType)
+export(withAll)
+export(withAny)
+export(withAtLeast)
+export(withAtMost)
+export(writeCohort)
+export(writeConceptSet)
+exportMethods("==")
+exportMethods(collectGuid)
+exportMethods(compile)
+import(dplyr)
+importFrom(DBI,dbGetQuery)
+importFrom(dplyr,across)
+importFrom(dplyr,filter)
+importFrom(dplyr,inner_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,select)
+importFrom(generics,compile)
+importFrom(magrittr,"%>%")
+importFrom(methods,"slot<-")
+importFrom(readr,read_csv)
+importFrom(readr,write_csv)
+importFrom(rlang,"%||%")
+importFrom(rlang,":=")
+importFrom(rlang,.data)