diff --git a/FourCePhase2.1Data/DESCRIPTION b/FourCePhase2.1Data/DESCRIPTION index 102b03d..b41525e 100644 --- a/FourCePhase2.1Data/DESCRIPTION +++ b/FourCePhase2.1Data/DESCRIPTION @@ -13,4 +13,5 @@ Description: What the package does (one paragraph). License: What license it uses Encoding: UTF-8 LazyData: true -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.2 +Roxygen: list(markdown = TRUE) diff --git a/FourCePhase2.1Data/NAMESPACE b/FourCePhase2.1Data/NAMESPACE index 5af79f4..99de5ff 100644 --- a/FourCePhase2.1Data/NAMESPACE +++ b/FourCePhase2.1Data/NAMESPACE @@ -6,30 +6,33 @@ importFrom(tidyr,spread) importFrom(survival,survfit,Surv,coxph) importFrom(stringr,str_to_title,str_trim) importFrom(data.table,data.table) + +export(get4ceFile) export(get4ceRootDirectoryName) +export(getClinicalCourse) +export(getClinicalCourse_nodocker) export(getContainerScratchDirectory) +export(getDailyCounts) +export(getDailyCounts_nodocker) +export(getDemographics) +export(getDemographics_nodocker) +export(getDiagnoses) +export(getDiagnoses_nodocker) export(getInputDataDirectoryName) -export(getSiteId) +export(getLabs) +export(getLabs_nodocker) export(getLocalPatientClinicalCourse) +export(getLocalPatientClinicalCourse_nodocker) +export(getLocalPatientMapping) +export(getLocalPatientMapping_nodocker) export(getLocalPatientObservations) +export(getLocalPatientObservations_nodocker) export(getLocalPatientSummary) -export(getLocalPatientMapping) -export(getLabs) +export(getLocalPatientSummary_nodocker) export(getMedications) -export(getDiagnoses) -export(getDemographics) -export(getDailyCounts) -export(getClinicalCourse) +export(getMedications_nodocker) export(getObfuscation) +export(getSiteId) export(runQC) -export(getLocalPatientClinicalCourse_nodocker) -export(getLocalPatientObservations_nodocker) -export(getLocalPatientSummary_nodocker) -export(getLocalPatientMapping_nodocker) -export(getLabs_nodocker) -export(getMedications_nodocker) -export(getDiagnoses_nodocker) -export(getDemographics_nodocker) -export(getDailyCounts_nodocker) -export(getClinicalCourse_nodocker) export(runQC_nodocker) +importFrom(utils,read.csv) diff --git a/FourCePhase2.1Data/R/getData.R b/FourCePhase2.1Data/R/getData.R index ed8a8c3..42a5126 100644 --- a/FourCePhase2.1Data/R/getData.R +++ b/FourCePhase2.1Data/R/getData.R @@ -1,70 +1,123 @@ -#' Obtain the phase2.1 data +#' Import a 4CE CSV file +#' +#' Files are loaded from the input data directory, optionally using [data.table::fread()]. +#' +#' @param filename Name of the file, such as LocalPatientSummary.csv +#' @param dir.input Input directory, which is via [getInputDataDirectoryName()] +#' if using docker. +#' @param fread if TRUE, use data.table::fread() for faster import. Otherwise +#' use read.csv(). This will also check the 4ce.fread option to make it work +#' without passing a function argument. +#' @param tolower Lowercase column names? (default: yes) +#' @param ... (Optional) Additional arguments passed through to fread() or +#' read.csv() #' -#' @keywords 4CE Phase2 Project +#' @seealso [data.table::fread()], [utils::read.csv()] +#' #' @export +#' @importFrom utils read.csv +get4ceFile <- + function(filename, + dir.input = getInputDataDirectoryName(), + fread = getOption("4ce.fread", FALSE), + tolower = TRUE, + ...) { + + filepath = file.path(dir.input, filename) + + if (fread) { + df = data.table::fread(filepath, data.table = FALSE, ...) + } else { + df = read.csv(filepath, ...) + } + + if (tolower) { + colnames(df) = tolower(colnames(df)) + } + + return(df) +} -getLocalPatientClinicalCourse<- function(siteid) { - dir.input=getInputDataDirectoryName() - LocalPatientClinicalCourse=read.csv(paste0(dir.input, "/LocalPatientClinicalCourse.csv")) - colnames(LocalPatientClinicalCourse)=tolower(colnames(LocalPatientClinicalCourse)) - LocalPatientClinicalCourse +#' Import LocalPatientClinicalCourse.csv +#' +#' Uses [get4ceFile()] - see that file for additional customization. +#' +#' @param siteid (unused) +#' @param ... (Optional) Additional arguments passed to [get4ceFile()]. +#' +#' @seealso [get4ceFile()] +#' @export +getLocalPatientClinicalCourse <- function(siteid = NULL, ...) { + get4ceFile("LocalPatientClinicalCourse.csv", ...) } -getLocalPatientObservations<- function(siteid) { - dir.input=getInputDataDirectoryName() - LocalPatientObservations=read.csv(paste0(dir.input, "/LocalPatientObservations.csv")) - colnames(LocalPatientObservations)=tolower(colnames(LocalPatientObservations)) - LocalPatientObservations +#' Import LocalPatientObservations.csv +#' @inherit getLocalPatientClinicalCourse +#' @export +getLocalPatientObservations <- function(siteid = NULL, ...) { + get4ceFile("LocalPatientObservations.csv", ...) } -getLocalPatientSummary<- function(siteid) { - dir.input=getInputDataDirectoryName() - LocalPatientSummary=read.csv(paste0(dir.input, "/LocalPatientSummary.csv")) - colnames(LocalPatientSummary)=tolower(colnames(LocalPatientSummary)) - LocalPatientSummary +#' Import LocalPatientSummary.csv +#' @inherit getLocalPatientClinicalCourse +#' @export +getLocalPatientSummary <- function(siteid = NULL, ...) { + get4ceFile("LocalPatientSummary.csv", ...) } -getLocalPatientMapping<- function(siteid) { - dir.input=getInputDataDirectoryName() - LocalPatientMapping=read.csv(paste0(dir.input, "/LocalPatientMapping.csv")) - colnames(LocalPatientMapping)=tolower(colnames(LocalPatientMapping)) - LocalPatientMapping +#' Import LocalPatientMapping.csv +#' @inherit getLocalPatientClinicalCourse +#' @export +getLocalPatientMapping<- function(siteid = NULL, ...) { + get4ceFile("LocalPatientMapping.csv", ...) } -getLabs<- function(siteid) { - dir.input=getInputDataDirectoryName() - Labs=read.csv(paste0(dir.input,"/Labs-", siteid,".csv")) - Labs +#' Import Labs-yoursite.csv +#' +#' Uses [get4ceFile()] - see that file for additional customization. +#' +#' @param siteid Name of your site. +#' @param ... (Optional) Additional arguments passed to [get4ceFile()]. +# +#' @seealso [get4ceFile()] +#' @export +getLabs<- function(siteid, ...) { + get4ceFile(paste0("Labs-", siteid, ".csv"), tolower = FALSE, ...) } -getMedications<- function(siteid) { - dir.input=getInputDataDirectoryName() - Medications=read.csv(paste0(dir.input,"/Medications-", siteid,".csv")) - Medications +#' Import Medications-yoursite.csv +#' @inherit getLabs +#' @export +getMedications<- function(siteid, ...) { + get4ceFile(paste0("Medications-", siteid, ".csv"), tolower = FALSE, ...) } -getDiagnoses<- function(siteid) { - dir.input=getInputDataDirectoryName() - Diagnoses=read.csv(paste0(dir.input,"/Diagnoses-", siteid,".csv")) - Diagnoses +#' Import Diagnoses-yoursite.csv +#' @inheritParams getLabs +#' @export +getDiagnoses<- function(siteid, ...) { + get4ceFile(paste0("Diagnoses-", siteid, ".csv"), tolower = FALSE, ...) } -getDemographics<- function(siteid) { - dir.input=getInputDataDirectoryName() - Demographics=read.csv(paste0(dir.input,"/Demographics-", siteid,".csv")) - Demographics +#' Import Demographics-yoursite.csv +#' @inheritParams getLabs +#' @export +getDemographics<- function(siteid, ...) { + get4ceFile(paste0("Demographics-", siteid, ".csv"), tolower = FALSE, ...) } -getDailyCounts<- function(siteid) { - dir.input=getInputDataDirectoryName() - DailyCounts=read.csv(paste0(dir.input,"/DailyCounts-", siteid,".csv")) - DailyCounts +#' Import DailyCounts-yoursite.csv +#' @inheritParams getLabs +#' @export +getDailyCounts<- function(siteid, ...) { + get4ceFile(paste0("DailyCounts-", siteid, ".csv"), tolower = FALSE, ...) } -getClinicalCourse<- function(siteid) { - dir.input=getInputDataDirectoryName() - ClinicalCourse=read.csv(paste0(dir.input,"/ClinicalCourse-", siteid,".csv")) - ClinicalCourse +#' Import ClinicalCourse-yoursite.csv +#' @inheritParams getLabs +#' @export +getClinicalCourse<- function(siteid, ...) { + get4ceFile(paste0("ClinicalCourse-", siteid, ".csv"), tolower = FALSE, ...) } diff --git a/FourCePhase2.1Data/R/getData_nodocker.R b/FourCePhase2.1Data/R/getData_nodocker.R index 22eefe0..2f625b3 100644 --- a/FourCePhase2.1Data/R/getData_nodocker.R +++ b/FourCePhase2.1Data/R/getData_nodocker.R @@ -1,60 +1,86 @@ - -#' Obtain the phase2.1 data -#' -#' @keywords 4CE Phase2 Project +#' Import LocaLPatientClinicalCourse.csv +#' +#' Uses [get4ceFile()] - see that file for additional customization. +#' +#' @param siteid Name of your site. +#' @param dir.input Input directory +#' @param ... (Optional) Additional arguments passed to [get4ceFile()]. +# +#' @seealso [get4ceFile()] #' @export - -getLocalPatientClinicalCourse_nodocker<- function(siteid, dir.input) { - LocalPatientClinicalCourse=read.csv(file.path(dir.input, "LocalPatientClinicalCourse.csv")) - colnames(LocalPatientClinicalCourse)=tolower(colnames(LocalPatientClinicalCourse)) - LocalPatientClinicalCourse +getLocalPatientClinicalCourse_nodocker <- function(siteid, dir.input, ...) { + get4ceFile("LocalPatientClinicalCourse.csv", dir.input, ...) } -getLocalPatientObservations_nodocker<- function(siteid, dir.input) { - LocalPatientObservations=read.csv(file.path(dir.input, "LocalPatientObservations.csv")) - colnames(LocalPatientObservations)=tolower(colnames(LocalPatientObservations)) - LocalPatientObservations + +#' Import LocaLPatientObservations.csv +#' @inherit getLocalPatientClinicalCourse_nodocker +#' @export +getLocalPatientObservations_nodocker <- function(siteid, dir.input, ...) { + get4ceFile("LocalPatientObservations.csv", dir.input, ...) } -getLocalPatientSummary_nodocker<- function(siteid, dir.input) { - LocalPatientSummary=read.csv(file.path(dir.input, "LocalPatientSummary.csv")) - colnames(LocalPatientSummary)=tolower(colnames(LocalPatientSummary)) - LocalPatientSummary +#' Import LocaLPatientSummary.csv +#' @inherit getLocalPatientClinicalCourse_nodocker +#' @export +getLocalPatientSummary_nodocker <- function(siteid, dir.input, ...) { + get4ceFile("LocalPatientSummary.csv", dir.input, ...) } -getLocalPatientMapping_nodocker<- function(siteid, dir.input) { - LocalPatientMapping=read.csv(file.path(dir.input, "LocalPatientMapping.csv")) - colnames(LocalPatientMapping)=tolower(colnames(LocalPatientMapping)) - LocalPatientMapping +#' Import LocaLPatientSummary.csv +#' @inherit getLocalPatientClinicalCourse_nodocker +#' @export +getLocalPatientMapping_nodocker <- function(siteid, dir.input, ...) { + get4ceFile("LocalPatientMapping.csv", dir.input, ...) } -getLabs_nodocker<- function(siteid,dir.input) { - Labs=read.csv(file.path(dir.input,paste0("Labs-", siteid,".csv"))) - Labs +#' Import Labs-yoursite.csv +#' +#' Uses [get4ceFile()] - see that file for additional customization. +#' +#' @param siteid Name of your site. +#' @param dir.input Input directory +#' @param ... (Optional) Additional arguments passed to [get4ceFile()]. +# +#' @seealso [get4ceFile()] +#' @export +getLabs_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("Labs-", siteid,".csv"), dir.input, tolower = FALSE, ...) } -getMedications_nodocker<- function(siteid,dir.input) { - Medications=read.csv(file.path(dir.input,paste0("Medications-", siteid,".csv"))) - Medications + +#' Import Medications-yoursite.csv +#' @inherit getLabs_nodocker +#' @export +getMedications_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("Medications-", siteid,".csv"), dir.input, tolower = FALSE, ...) } -getDiagnoses_nodocker<- function(siteid,dir.input) { - Diagnoses=read.csv(file.path(dir.input,paste0("Diagnoses-", siteid,".csv"))) - Diagnoses +#' Import Diagnoses-yoursite.csv +#' @inherit getLabs_nodocker +#' @export +getDiagnoses_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("Diagnoses-", siteid,".csv"), dir.input, tolower = FALSE, ...) } -getDemographics_nodocker<- function(siteid,dir.input) { - Demographics=read.csv(file.path(dir.input,paste0("Demographics-", siteid,".csv"))) - Demographics +#' Import Demographics-yoursite.csv +#' @inherit getLabs_nodocker +#' @export +getDemographics_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("Demographics-", siteid,".csv"), dir.input, tolower = FALSE, ...) } -getDailyCounts_nodocker<- function(siteid,dir.input) { - DailyCounts=read.csv(file.path(dir.input,paste0("DailyCounts-", siteid,".csv"))) - DailyCounts +#' Import DailyCounts-yoursite.csv +#' @inherit getLabs_nodocker +#' @export +getDailyCounts_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("DailyCounts-", siteid,".csv"), dir.input, tolower = FALSE, ...) } -getClinicalCourse_nodocker<- function(siteid,dir.input) { - ClinicalCourse=read.csv(file.path(dir.input,paste0("ClinicalCourse-", siteid,".csv"))) - ClinicalCourse +#' Import ClinicalCourse-yoursite.csv +#' @inherit getLabs_nodocker +#' @export +getClinicalCourse_nodocker <- function(siteid, dir.input, ...) { + get4ceFile(paste0("ClinicalCourse-", siteid,".csv"), dir.input, tolower = FALSE, ...) } diff --git a/FourCePhase2.1Data/man/get4ceFile.Rd b/FourCePhase2.1Data/man/get4ceFile.Rd new file mode 100644 index 0000000..e20ea33 --- /dev/null +++ b/FourCePhase2.1Data/man/get4ceFile.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{get4ceFile} +\alias{get4ceFile} +\title{Import a 4CE CSV file} +\usage{ +get4ceFile( + filename, + dir.input = getInputDataDirectoryName(), + fread = getOption("4ce.fread", FALSE), + tolower = TRUE, + ... +) +} +\arguments{ +\item{filename}{Name of the file, such as LocalPatientSummary.csv} + +\item{dir.input}{Input directory, which is via \code{\link[=getInputDataDirectoryName]{getInputDataDirectoryName()}} +if using docker.} + +\item{fread}{if TRUE, use data.table::fread() for faster import. Otherwise +use read.csv(). This will also check the 4ce.fread option to make it work +without passing a function argument.} + +\item{tolower}{Lowercase column names? (default: yes)} + +\item{...}{(Optional) Additional arguments passed through to fread() or +read.csv()} +} +\description{ +Files are loaded from the input data directory, optionally using \code{\link[data.table:fread]{data.table::fread()}}. +} +\seealso{ +\code{\link[data.table:fread]{data.table::fread()}}, \code{\link[utils:read.table]{utils::read.csv()}} +} diff --git a/FourCePhase2.1Data/man/getClinicalCourse.Rd b/FourCePhase2.1Data/man/getClinicalCourse.Rd new file mode 100644 index 0000000..ffe92f5 --- /dev/null +++ b/FourCePhase2.1Data/man/getClinicalCourse.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getClinicalCourse} +\alias{getClinicalCourse} +\title{Import ClinicalCourse-yoursite.csv} +\usage{ +getClinicalCourse(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Import ClinicalCourse-yoursite.csv +} diff --git a/FourCePhase2.1Data/man/getClinicalCourse_nodocker.Rd b/FourCePhase2.1Data/man/getClinicalCourse_nodocker.Rd new file mode 100644 index 0000000..39a82c2 --- /dev/null +++ b/FourCePhase2.1Data/man/getClinicalCourse_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getClinicalCourse_nodocker} +\alias{getClinicalCourse_nodocker} +\title{Import ClinicalCourse-yoursite.csv} +\usage{ +getClinicalCourse_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getDailyCounts.Rd b/FourCePhase2.1Data/man/getDailyCounts.Rd new file mode 100644 index 0000000..595d2b2 --- /dev/null +++ b/FourCePhase2.1Data/man/getDailyCounts.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getDailyCounts} +\alias{getDailyCounts} +\title{Import DailyCounts-yoursite.csv} +\usage{ +getDailyCounts(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Import DailyCounts-yoursite.csv +} diff --git a/FourCePhase2.1Data/man/getDailyCounts_nodocker.Rd b/FourCePhase2.1Data/man/getDailyCounts_nodocker.Rd new file mode 100644 index 0000000..23046b3 --- /dev/null +++ b/FourCePhase2.1Data/man/getDailyCounts_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getDailyCounts_nodocker} +\alias{getDailyCounts_nodocker} +\title{Import DailyCounts-yoursite.csv} +\usage{ +getDailyCounts_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getDemographics.Rd b/FourCePhase2.1Data/man/getDemographics.Rd new file mode 100644 index 0000000..4eec183 --- /dev/null +++ b/FourCePhase2.1Data/man/getDemographics.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getDemographics} +\alias{getDemographics} +\title{Import Demographics-yoursite.csv} +\usage{ +getDemographics(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Import Demographics-yoursite.csv +} diff --git a/FourCePhase2.1Data/man/getDemographics_nodocker.Rd b/FourCePhase2.1Data/man/getDemographics_nodocker.Rd new file mode 100644 index 0000000..6fc5a2a --- /dev/null +++ b/FourCePhase2.1Data/man/getDemographics_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getDemographics_nodocker} +\alias{getDemographics_nodocker} +\title{Import Demographics-yoursite.csv} +\usage{ +getDemographics_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getDiagnoses.Rd b/FourCePhase2.1Data/man/getDiagnoses.Rd new file mode 100644 index 0000000..93f925e --- /dev/null +++ b/FourCePhase2.1Data/man/getDiagnoses.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getDiagnoses} +\alias{getDiagnoses} +\title{Import Diagnoses-yoursite.csv} +\usage{ +getDiagnoses(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Import Diagnoses-yoursite.csv +} diff --git a/FourCePhase2.1Data/man/getDiagnoses_nodocker.Rd b/FourCePhase2.1Data/man/getDiagnoses_nodocker.Rd new file mode 100644 index 0000000..fe199c3 --- /dev/null +++ b/FourCePhase2.1Data/man/getDiagnoses_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getDiagnoses_nodocker} +\alias{getDiagnoses_nodocker} +\title{Import Diagnoses-yoursite.csv} +\usage{ +getDiagnoses_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLabs.Rd b/FourCePhase2.1Data/man/getLabs.Rd new file mode 100644 index 0000000..728e287 --- /dev/null +++ b/FourCePhase2.1Data/man/getLabs.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getLabs} +\alias{getLabs} +\title{Import Labs-yoursite.csv} +\usage{ +getLabs(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLabs_nodocker.Rd b/FourCePhase2.1Data/man/getLabs_nodocker.Rd new file mode 100644 index 0000000..0b35e8e --- /dev/null +++ b/FourCePhase2.1Data/man/getLabs_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getLabs_nodocker} +\alias{getLabs_nodocker} +\title{Import Labs-yoursite.csv} +\usage{ +getLabs_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientClinicalCourse.Rd b/FourCePhase2.1Data/man/getLocalPatientClinicalCourse.Rd new file mode 100644 index 0000000..96caf54 --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientClinicalCourse.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getLocalPatientClinicalCourse} +\alias{getLocalPatientClinicalCourse} +\title{Import LocalPatientClinicalCourse.csv} +\usage{ +getLocalPatientClinicalCourse(siteid = NULL, ...) +} +\arguments{ +\item{siteid}{(unused)} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientClinicalCourse_nodocker.Rd b/FourCePhase2.1Data/man/getLocalPatientClinicalCourse_nodocker.Rd new file mode 100644 index 0000000..ecf8644 --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientClinicalCourse_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getLocalPatientClinicalCourse_nodocker} +\alias{getLocalPatientClinicalCourse_nodocker} +\title{Import LocaLPatientClinicalCourse.csv} +\usage{ +getLocalPatientClinicalCourse_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientMapping.Rd b/FourCePhase2.1Data/man/getLocalPatientMapping.Rd new file mode 100644 index 0000000..91b255f --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientMapping.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getLocalPatientMapping} +\alias{getLocalPatientMapping} +\title{Import LocalPatientMapping.csv} +\usage{ +getLocalPatientMapping(siteid = NULL, ...) +} +\arguments{ +\item{siteid}{(unused)} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientMapping_nodocker.Rd b/FourCePhase2.1Data/man/getLocalPatientMapping_nodocker.Rd new file mode 100644 index 0000000..658d72b --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientMapping_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getLocalPatientMapping_nodocker} +\alias{getLocalPatientMapping_nodocker} +\title{Import LocaLPatientSummary.csv} +\usage{ +getLocalPatientMapping_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientObservations.Rd b/FourCePhase2.1Data/man/getLocalPatientObservations.Rd new file mode 100644 index 0000000..dd92fe9 --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientObservations.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getLocalPatientObservations} +\alias{getLocalPatientObservations} +\title{Import LocalPatientObservations.csv} +\usage{ +getLocalPatientObservations(siteid = NULL, ...) +} +\arguments{ +\item{siteid}{(unused)} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientObservations_nodocker.Rd b/FourCePhase2.1Data/man/getLocalPatientObservations_nodocker.Rd new file mode 100644 index 0000000..5666d7b --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientObservations_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getLocalPatientObservations_nodocker} +\alias{getLocalPatientObservations_nodocker} +\title{Import LocaLPatientObservations.csv} +\usage{ +getLocalPatientObservations_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientSummary.Rd b/FourCePhase2.1Data/man/getLocalPatientSummary.Rd new file mode 100644 index 0000000..2a3efaf --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientSummary.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getLocalPatientSummary} +\alias{getLocalPatientSummary} +\title{Import LocalPatientSummary.csv} +\usage{ +getLocalPatientSummary(siteid = NULL, ...) +} +\arguments{ +\item{siteid}{(unused)} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getLocalPatientSummary_nodocker.Rd b/FourCePhase2.1Data/man/getLocalPatientSummary_nodocker.Rd new file mode 100644 index 0000000..6b1faf7 --- /dev/null +++ b/FourCePhase2.1Data/man/getLocalPatientSummary_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getLocalPatientSummary_nodocker} +\alias{getLocalPatientSummary_nodocker} +\title{Import LocaLPatientSummary.csv} +\usage{ +getLocalPatientSummary_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getMedications.Rd b/FourCePhase2.1Data/man/getMedications.Rd new file mode 100644 index 0000000..3cdcc0a --- /dev/null +++ b/FourCePhase2.1Data/man/getMedications.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData.R +\name{getMedications} +\alias{getMedications} +\title{Import Medications-yoursite.csv} +\usage{ +getMedications(siteid, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/FourCePhase2.1Data/man/getMedications_nodocker.Rd b/FourCePhase2.1Data/man/getMedications_nodocker.Rd new file mode 100644 index 0000000..221a791 --- /dev/null +++ b/FourCePhase2.1Data/man/getMedications_nodocker.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/getData_nodocker.R +\name{getMedications_nodocker} +\alias{getMedications_nodocker} +\title{Import Medications-yoursite.csv} +\usage{ +getMedications_nodocker(siteid, dir.input, ...) +} +\arguments{ +\item{siteid}{Name of your site.} + +\item{dir.input}{Input directory} + +\item{...}{(Optional) Additional arguments passed to \code{\link[=get4ceFile]{get4ceFile()}}.} +} +\description{ +Uses \code{\link[=get4ceFile]{get4ceFile()}} - see that file for additional customization. +} +\seealso{ +\code{\link[=get4ceFile]{get4ceFile()}} +} diff --git a/Phase2.1DataRPackage.Rproj b/Phase2.1DataRPackage.Rproj index 8e3c2eb..85a2b86 100644 --- a/Phase2.1DataRPackage.Rproj +++ b/Phase2.1DataRPackage.Rproj @@ -11,3 +11,9 @@ Encoding: UTF-8 RnwWeave: Sweave LaTeX: pdfLaTeX + +BuildType: Package +PackageUseDevtools: Yes +PackagePath: FourCePhase2.1Data +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace