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Merge pull request #2 from thehyve/feature
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@@ -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$ |
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# 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() | ||
} |
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.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 |
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@@ -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 |
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Original file line number | Diff line number | Diff line change |
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@@ -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) |
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