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