R/load.data.r
In qPharmetra/qpToolkit: qPharmetra R Tools
Defines functions
load.data
Documented in
load.data
# name: load.data
# purpose: read data for an analysis from a variety of external typical file types, and assign them
# to archival and working datasets in R.
# input: a list of files, their names, R object names to assign them to, and the input director
# in wihch these are found. NOTE the function an also be used to do a "scan" for ANY files
# in this folder and load them without being specified. Filetypes supported include SAS xpt,
# Microsoft Excel (xls and xlsx), Comma Separated Values (csv), and tab files (tab).
# output: R objects
# note:
# ROXYGEN Documentation
#' Loading data of various formats
#' @description Read data for an analysis from a variety of external typical file types, and assign them
# to archival and working datasets in R. The function takes SAS transport (XPT), Microsoft Excel (XLS, XLSX), comma-delimited (CSV) and tab-delimited (ASCII) formats. NOTE the function an also be used to do a "scan" for ANY files in this folder and load them without being specified.
#' @param xptFiles vector of SAS transport (XPT) filenames
#' @param xlsFiles vector of Microsoft Excel (XLS, XLSX) filenames
#' @param csvFiles vector of comma-delimited (CSV) filenames
#' @param tabFiles vector of tab-delimited (ASCII) filenames
#' @param dir directory where the files reside
#' @param xptNames vector of object names for each SAS transport (XPT) file, in the same order.
#' @param xlsNames vector of object names for each Microsoft Excel (XLS, XLSX) file, in the same order.
#' @param csvNames vector of object names for each comma-delimited (CSV) file, in the same order
#' @param tabNames vector of object names for each tab-delimited (ASCII) file, in the same order
#' @param perl directory where the perl executable resides
#' @param xlsSheets a numeric vector of \code{length(xlsFiles)} defining which sheet in the workbook needs to be read. If you do not specify this, by default the first sheet of each workbook will be read.
#' @param doScan logical
#' @param target.env environment The environment into which the data files will be loaded
#' and attached.
#' @return Placeholder for return description
#' @export
#' @importFrom gdata read.xls
#' @importFrom foreign read.xport
#' @importFrom utils read.csv
#' @importFrom utils read.delim
#' @examples
#' \dontrun{
#' load.data(xlsFiles = "ExampleInput.xlsx",
#' xlsNames = "XLinput1",
#' xlsSheets = 1, doScan = FALSE)
#' head(XLinput1)
#' head(iXLinput1)
#' load.data(xlsFiles = "ExampleInput.xlsx",
#' xlsNames = "XLinput2",
#' xlsSheets = 2, # NOTE We can specify which worksheet (tab) of the Excel file
#' doScan = FALSE)
#' head(iXLinput2)
# Exammple of providing a LIST of files to import
#' load.data(csvFiles = c("ExampleInput2.csv","ExampleInput3.csv"),
#' csvNames = c("CSVinput1", "CSVinput2"),
#' doScan = FALSE)
#' head(CSVinput1)
#' load.data() # loading JUST doing automatic search for files ("scan")
#' }
load.data <- function(xptFiles, xlsFiles, csvFiles, tabFiles,
dir = "../project input/client data/data",
xlsNames, xptNames, csvNames, tabNames, perl = "C:/Perl64/bin/perl.exe",
xlsSheets, doScan = TRUE, target.env = parent.frame()) {
if(!missing(xptNames)) {
if(missing(xptFiles)|length(xptNames)!=length(xptFiles)) {
stop(paste("xptNames cannot be defined unless a list of xptFiles of equal length",
"is also specified"))
}
}
if(!missing(xlsNames)) {
if(missing(xlsFiles)|length(xlsNames)!=length(xlsFiles)) {
stop(paste("xlsNames cannot be defined unless a list of xlsFiles of equal length",
"is also specified"))
}
if(!missing(xlsSheets)) {
if(length(xlsSheets)!=length(xlsFiles)) {
stop(paste("xlsSheets cannot be defined unless it has equal length to xlsFiles"))
}
}
else {
xlsSheets = rep(1,length(xlsFiles))
}
}
if(!missing(csvNames)) {
if(missing(csvFiles)|length(csvNames)!=length(csvFiles)) {
stop(paste("csvNames cannot be defined unless a list of csvFiles of equal length",
"is also specified"))
}
}
if(!missing(tabNames)) {
if(missing(tabFiles)|length(tabNames)!=length(tabFiles)) {
stop(paste("tabNames cannot be defined unless a list of tabFiles of equal length",
"is also specified"))
}
}
if (doScan) { # do scan
## Scan directory if no file list was provided
if(missing(xptFiles)) {
xptFiles = list.files(dir)
xptFiles = xptFiles[grep(".xpt", xptFiles)]
}
if(missing(xlsFiles)) {
xlsFiles = list.files(dir)
xlsFiles = xlsFiles[grep(".xls[x]*", xlsFiles)]
## remove files starting with "~" (temporary excel files)
xlsFiles = xlsFiles[!grepl("^~",xlsFiles)]
xlsSheets = rep(1,length(xlsFiles)) # default
}
if(missing(csvFiles)) {
csvFiles = list.files(dir)
csvFiles = csvFiles[grep(".csv", csvFiles)]
}
if(missing(tabFiles)) {
tabFiles = list.files(dir)
tabFiles = tabFiles[grep(".tab", tabFiles)]
}
if(missing(xptNames)) {
xptNames = sub("(.*).xpt","\\1",xptFiles)
}
if(missing(xlsNames)) {
xlsNames = sub("(.*).xls[x]*","\\1",xlsFiles)
}
if(missing(csvNames)) {
csvNames = sub("(.*).csv","\\1",csvFiles)
}
if(missing(tabNames)) {
tabNames = sub("(.*).tab","\\1",tabFiles)
}
}
else { # do not do scan,
# but must establish variables if missing, for use below
if (missing(xptFiles)) xptFiles = NULL
if (missing(xlsFiles)) xlsFiles = NULL
if (missing(csvFiles)) csvFiles = NULL
if (missing(tabFiles)) tabFiles = NULL
}
if(length(xptFiles)>0) { # LH
for(i in 1:length(xptFiles)) {
# fileData = read.xport(paste(dir,xptFiles[i], sep = "/"),as.is = T) KD 18th October 2013
fileData = foreign::read.xport(paste(dir,xptFiles[i], sep = "/"))
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", xptNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(xptNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",xptNames[i],sep = ""))
}
}
if(length(xlsFiles)>0) { # LH
for(i in 1:length(xlsFiles)) {
fileData = read.xls(paste(dir,xlsFiles[i], sep = "/"), perl = perl, sheet = xlsSheets[i])
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", xlsNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(xlsNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",xlsNames[i],sep = ""))
}
}
if(length(csvFiles)>0) { # LH
for(i in 1:length(csvFiles)) {
fileData = read.csv(paste(dir,csvFiles[i], sep = "/"), as.is = TRUE)
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", csvNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(csvNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",csvNames[i],sep = ""))
}
}
if(length(tabFiles)>0) { # LH
for(i in 1:length(tabFiles)) {
fileData = read.delim(paste(dir,tabFiles[i], sep = "/"), as.is = TRUE)
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", tabNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(tabNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",tabNames[i],sep = ""))
}
}
}
if (F) {
load.data(xlsFiles = "ExampleInput.xlsx",
xlsNames = "XLinput1",
xlsSheets = 1, doScan = FALSE)
#[1] "Created data frame XLinput1"
head(XLinput1)
#a b c d rec.id
#1 29 10.779126 a -9.962622 1
#2 24 19.237118 a 15.411355 2
#3 29 16.632331 b 7.596994 3
#4 28 2.927655 c -33.517035 4
#5 28 33.271880 c 57.515641 5
#6 21 22.987656 c 26.662967 6
head(iXLinput1)
#a b c d rec.id
#1 29 10.779126 a -9.962622 1
#2 24 19.237118 a 15.411355 2
#3 29 16.632331 b 7.596994 3
#4 28 2.927655 c -33.517035 4
#5 28 33.271880 c 57.515641 5
#6 21 22.987656 c 26.662967 6
load.data(xlsFiles = "ExampleInput.xlsx",
xlsNames = "XLinput2",
xlsSheets = 2, # NOTE WE can specify which worksheet (tab) of the Excel file
doScan = FALSE)
head(iXLinput2)
# e f g h rec.id
# 1 130 43.64459 a 83.24640 1
# 2 127 44.20029 a 83.92436 2
# 3 117 53.74561 b 95.56964 3
# 4 101 44.77443 c 84.62481 4
# 5 105 54.66527 c 96.69163 5
# 6 117 52.22399 c 93.71326 6
# Exammple of providing a LIST of files to import
load.data(csvFiles = c("ExampleInput2.csv","ExampleInput3.csv"),
csvNames = c("CSVinput1", "CSVinput2"),
doScan = FALSE)
#[1] "Created data frame CSVinput1"
#[1] "Created data frame CSVinput2"
head(CSVinput1)
# i j k l rec.id
# 1 12 1.4278484 a 21.17344 1
# 2 13 25.7748203 a 123.39071 2
# 3 10 17.5700167 b 82.36330 3
# 4 19 27.6167870 c 116.69581 4
# 5 28 27.3402980 c 119.13643 5
# 6 17 0.3835043 c 13.86611 6
load.data() # loading JUST doing automatic search for files ("scan")
}
qPharmetra/qpToolkit documentation built on May 24, 2023, 8:52 a.m.
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Defines functions load.data
Documented in load.data
# name: load.data
# purpose: read data for an analysis from a variety of external typical file types, and assign them
# to archival and working datasets in R.
# input: a list of files, their names, R object names to assign them to, and the input director
# in wihch these are found. NOTE the function an also be used to do a "scan" for ANY files
# in this folder and load them without being specified. Filetypes supported include SAS xpt,
# Microsoft Excel (xls and xlsx), Comma Separated Values (csv), and tab files (tab).
# output: R objects
# note:
# ROXYGEN Documentation
#' Loading data of various formats
#' @description Read data for an analysis from a variety of external typical file types, and assign them
# to archival and working datasets in R. The function takes SAS transport (XPT), Microsoft Excel (XLS, XLSX), comma-delimited (CSV) and tab-delimited (ASCII) formats. NOTE the function an also be used to do a "scan" for ANY files in this folder and load them without being specified.
#' @param xptFiles vector of SAS transport (XPT) filenames
#' @param xlsFiles vector of Microsoft Excel (XLS, XLSX) filenames
#' @param csvFiles vector of comma-delimited (CSV) filenames
#' @param tabFiles vector of tab-delimited (ASCII) filenames
#' @param dir directory where the files reside
#' @param xptNames vector of object names for each SAS transport (XPT) file, in the same order.
#' @param xlsNames vector of object names for each Microsoft Excel (XLS, XLSX) file, in the same order.
#' @param csvNames vector of object names for each comma-delimited (CSV) file, in the same order
#' @param tabNames vector of object names for each tab-delimited (ASCII) file, in the same order
#' @param perl directory where the perl executable resides
#' @param xlsSheets a numeric vector of \code{length(xlsFiles)} defining which sheet in the workbook needs to be read. If you do not specify this, by default the first sheet of each workbook will be read.
#' @param doScan logical
#' @param target.env environment The environment into which the data files will be loaded
#' and attached.
#' @return Placeholder for return description
#' @export
#' @importFrom gdata read.xls
#' @importFrom foreign read.xport
#' @importFrom utils read.csv
#' @importFrom utils read.delim
#' @examples
#' \dontrun{
#' load.data(xlsFiles = "ExampleInput.xlsx",
#' xlsNames = "XLinput1",
#' xlsSheets = 1, doScan = FALSE)
#' head(XLinput1)
#' head(iXLinput1)
#' load.data(xlsFiles = "ExampleInput.xlsx",
#' xlsNames = "XLinput2",
#' xlsSheets = 2, # NOTE We can specify which worksheet (tab) of the Excel file
#' doScan = FALSE)
#' head(iXLinput2)
# Exammple of providing a LIST of files to import
#' load.data(csvFiles = c("ExampleInput2.csv","ExampleInput3.csv"),
#' csvNames = c("CSVinput1", "CSVinput2"),
#' doScan = FALSE)
#' head(CSVinput1)
#' load.data() # loading JUST doing automatic search for files ("scan")
#' }
load.data <- function(xptFiles, xlsFiles, csvFiles, tabFiles,
dir = "../project input/client data/data",
xlsNames, xptNames, csvNames, tabNames, perl = "C:/Perl64/bin/perl.exe",
xlsSheets, doScan = TRUE, target.env = parent.frame()) {
if(!missing(xptNames)) {
if(missing(xptFiles)|length(xptNames)!=length(xptFiles)) {
stop(paste("xptNames cannot be defined unless a list of xptFiles of equal length",
"is also specified"))
}
}
if(!missing(xlsNames)) {
if(missing(xlsFiles)|length(xlsNames)!=length(xlsFiles)) {
stop(paste("xlsNames cannot be defined unless a list of xlsFiles of equal length",
"is also specified"))
}
if(!missing(xlsSheets)) {
if(length(xlsSheets)!=length(xlsFiles)) {
stop(paste("xlsSheets cannot be defined unless it has equal length to xlsFiles"))
}
}
else {
xlsSheets = rep(1,length(xlsFiles))
}
}
if(!missing(csvNames)) {
if(missing(csvFiles)|length(csvNames)!=length(csvFiles)) {
stop(paste("csvNames cannot be defined unless a list of csvFiles of equal length",
"is also specified"))
}
}
if(!missing(tabNames)) {
if(missing(tabFiles)|length(tabNames)!=length(tabFiles)) {
stop(paste("tabNames cannot be defined unless a list of tabFiles of equal length",
"is also specified"))
}
}
if (doScan) { # do scan
## Scan directory if no file list was provided
if(missing(xptFiles)) {
xptFiles = list.files(dir)
xptFiles = xptFiles[grep(".xpt", xptFiles)]
}
if(missing(xlsFiles)) {
xlsFiles = list.files(dir)
xlsFiles = xlsFiles[grep(".xls[x]*", xlsFiles)]
## remove files starting with "~" (temporary excel files)
xlsFiles = xlsFiles[!grepl("^~",xlsFiles)]
xlsSheets = rep(1,length(xlsFiles)) # default
}
if(missing(csvFiles)) {
csvFiles = list.files(dir)
csvFiles = csvFiles[grep(".csv", csvFiles)]
}
if(missing(tabFiles)) {
tabFiles = list.files(dir)
tabFiles = tabFiles[grep(".tab", tabFiles)]
}
if(missing(xptNames)) {
xptNames = sub("(.*).xpt","\\1",xptFiles)
}
if(missing(xlsNames)) {
xlsNames = sub("(.*).xls[x]*","\\1",xlsFiles)
}
if(missing(csvNames)) {
csvNames = sub("(.*).csv","\\1",csvFiles)
}
if(missing(tabNames)) {
tabNames = sub("(.*).tab","\\1",tabFiles)
}
}
else { # do not do scan,
# but must establish variables if missing, for use below
if (missing(xptFiles)) xptFiles = NULL
if (missing(xlsFiles)) xlsFiles = NULL
if (missing(csvFiles)) csvFiles = NULL
if (missing(tabFiles)) tabFiles = NULL
}
if(length(xptFiles)>0) { # LH
for(i in 1:length(xptFiles)) {
# fileData = read.xport(paste(dir,xptFiles[i], sep = "/"),as.is = T) KD 18th October 2013
fileData = foreign::read.xport(paste(dir,xptFiles[i], sep = "/"))
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", xptNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(xptNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",xptNames[i],sep = ""))
}
}
if(length(xlsFiles)>0) { # LH
for(i in 1:length(xlsFiles)) {
fileData = read.xls(paste(dir,xlsFiles[i], sep = "/"), perl = perl, sheet = xlsSheets[i])
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", xlsNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(xlsNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",xlsNames[i],sep = ""))
}
}
if(length(csvFiles)>0) { # LH
for(i in 1:length(csvFiles)) {
fileData = read.csv(paste(dir,csvFiles[i], sep = "/"), as.is = TRUE)
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", csvNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(csvNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",csvNames[i],sep = ""))
}
}
if(length(tabFiles)>0) { # LH
for(i in 1:length(tabFiles)) {
fileData = read.delim(paste(dir,tabFiles[i], sep = "/"), as.is = TRUE)
names(fileData) = tolower(names(fileData))
fileData$rec.id = 1:nrow(fileData)
assign(paste("i", tabNames[i], sep = ""), fileData,
envir = target.env) # Archival copy of the data
assign(tabNames[i], fileData,
envir = target.env) # Working copy
print(paste("Created data frame ",tabNames[i],sep = ""))
}
}
}
if (F) {
load.data(xlsFiles = "ExampleInput.xlsx",
xlsNames = "XLinput1",
xlsSheets = 1, doScan = FALSE)
#[1] "Created data frame XLinput1"
head(XLinput1)
#a b c d rec.id
#1 29 10.779126 a -9.962622 1
#2 24 19.237118 a 15.411355 2
#3 29 16.632331 b 7.596994 3
#4 28 2.927655 c -33.517035 4
#5 28 33.271880 c 57.515641 5
#6 21 22.987656 c 26.662967 6
head(iXLinput1)
#a b c d rec.id
#1 29 10.779126 a -9.962622 1
#2 24 19.237118 a 15.411355 2
#3 29 16.632331 b 7.596994 3
#4 28 2.927655 c -33.517035 4
#5 28 33.271880 c 57.515641 5
#6 21 22.987656 c 26.662967 6
load.data(xlsFiles = "ExampleInput.xlsx",
xlsNames = "XLinput2",
xlsSheets = 2, # NOTE WE can specify which worksheet (tab) of the Excel file
doScan = FALSE)
head(iXLinput2)
# e f g h rec.id
# 1 130 43.64459 a 83.24640 1
# 2 127 44.20029 a 83.92436 2
# 3 117 53.74561 b 95.56964 3
# 4 101 44.77443 c 84.62481 4
# 5 105 54.66527 c 96.69163 5
# 6 117 52.22399 c 93.71326 6
# Exammple of providing a LIST of files to import
load.data(csvFiles = c("ExampleInput2.csv","ExampleInput3.csv"),
csvNames = c("CSVinput1", "CSVinput2"),
doScan = FALSE)
#[1] "Created data frame CSVinput1"
#[1] "Created data frame CSVinput2"
head(CSVinput1)
# i j k l rec.id
# 1 12 1.4278484 a 21.17344 1
# 2 13 25.7748203 a 123.39071 2
# 3 10 17.5700167 b 82.36330 3
# 4 19 27.6167870 c 116.69581 4
# 5 28 27.3402980 c 119.13643 5
# 6 17 0.3835043 c 13.86611 6
load.data() # loading JUST doing automatic search for files ("scan")
}
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