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Merge pull request #12 from thehyve/update_post_capr_demo
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Update post capr demo
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guuswilmink authored Sep 20, 2024
2 parents 706d0dc + c67de7f commit 60ff9f4
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Showing 107 changed files with 3,538 additions and 3,332 deletions.
42 changes: 22 additions & 20 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -1,20 +1,22 @@
^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$
^requirements\.txt$
^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$
^data-raw$
3 changes: 3 additions & 0 deletions .Rprofile
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Expand Up @@ -10,5 +10,8 @@ if (any(list.files() == "renv")) {
} 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'")
if (!require("renv", quietly = TRUE)) {
utils::install.packages("renv")
}
renv::init()
}
24 changes: 5 additions & 19 deletions .gitignore
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Expand Up @@ -12,22 +12,8 @@ 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
data-raw
*config.yml
renv/
*.py
process_ucs.R
File renamed without changes.
6 changes: 4 additions & 2 deletions DESCRIPTION
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@@ -1,4 +1,4 @@
Package: Capr-PHEMS
Package: CaprPHEMS
Title: Cohort Definition Application Programming - project specific for PHEMS
Version: 2.0.8
Authors@R: c(
Expand Down Expand Up @@ -67,9 +67,11 @@ Collate:
'exit.R'
'cohort.R'
'collectCodesetId.R'
'conceptSets.R'
'countOccurrences.R'
'data.R'
'isStandard.R'
'isStandardCS.R'
'isStandardDB.R'
'table_linked_to_concept_field.R'
'utils.R'
LazyData: true
206 changes: 106 additions & 100 deletions NAMESPACE
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@@ -1,100 +1,106 @@
# 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)
# 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(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(isStandardDB)
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(DatabaseConnector,connect)
importFrom(DatabaseConnector,disconnect)
importFrom(DatabaseConnector,querySql)
importFrom(SqlRender,render)
importFrom(SqlRender,translate)
importFrom(dplyr,across)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
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)
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