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### This file is part of the 'foreign' package for R.
### R/read.epiinfo.R
### (c) 2002-4 Thomas Lumley
### Patches (c) 2002 Mark Myatt
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
read.epiinfo <- function (file, read.deleted = FALSE,
guess.broken.dates = FALSE, thisyear = NULL,
lower.case.names = FALSE)
{
if (is.character(file)) {
file <- file(file, "rt")
on.exit(close(file))
}
if (!inherits(file, "connection"))
stop("argument 'file' must be a character string or connection")
if (!isOpen(file)) {
open(file, "rt")
on.exit(close(file))
}
line <- readLines(file, 1L, ok = TRUE)
headerlength <- na.omit(sapply(strsplit(line, " ")[[1L]], as.numeric))[1L]
if (headerlength <= 0L)
stop("file has zero or fewer variables: probably not an EpiInfo file")
headerlines <- readLines(file, n = headerlength)
pushBack(headerlines, file)
comments <- sapply(headerlines, function(s) substring(s, 46L, 46L + 80L))
#
# Added comment = "" to fix '#' as entrychar being read as a comment
#
header <- scan(file, nlines = headerlength,
what = list(name = "", x = 0, y = 0, color = 0, x1 = 0,
y1 = 0, type = 0, len = 0, color = 0),
flush = TRUE, quiet = TRUE, comment = "")
header <- as.data.frame(lapply(header, I))
header$start <- cumsum(c(1L, header$len))[1L:headerlength]
header$stop <- cumsum(header$len)
multiline <- ceiling(max(header$stop) / 78L)
really.variables <- header$len != 0
header <- header[really.variables, ]
entrychar <- substr(header$name, 1L, 1L)
if (all(entrychar %in% c("#", "_")))
header$name <- substr(header$name, 2L, 12L)
comments <- comments[really.variables]
#
# Added support for EpiData introduced field types:
#
# 12 Automatic ID number fields (treated as numeric)
# 16 European (i.e. dd/mm/yyyy) format automatic date
# 17 SOUNDEX field
#
numbers <- (header$len > 0L) & ((header$type %in% c(0L, 6L, 12L)) | (header$type > 12L)) & !(header$type %in% c(16L, 17L))
datalines <- scan(file, what = "", sep = "\n", quote = "", quiet = TRUE, blank.lines.skip = TRUE, comment = "")
#
# Added check for empty file
#
if (length(datalines) == 0L)
stop("no records in file")
if (length(datalines)%%multiline)
warning("wrong number of records")
datalines <- matrix(datalines, nrow = multiline)
if (multiline > 1L)
datalines[-multiline, ] <- substr(datalines[-multiline, ], 1L, 78L)
datalines <- apply(datalines, 2L, paste, collapse = "")
deleted <- substr(datalines, nchar(datalines), nchar(datalines)) == "?"
nvars <- NROW(header)
data <- as.data.frame(lapply(1L:nvars, function(i) I(substring(datalines, header$start[i], header$stop[i]))))
names(data) <- header$name
names(comments) <- header$name
if (is.na(read.deleted))
data[deleted, ] <- NA
else if (!read.deleted)
data <- data[!deleted, ]
if (guess.broken.dates && is.null(thisyear))
thisyear <- format(Sys.time(), format = "%Y")
#
# Added support for field types:
#
# 10 US (i.e. mm/dd/yyyy) format field (EpiInfo)
# 12 Automatic ID number (treated as numeric)
# 16 European (i.e. dd/mm/yyyy) format automatic date (EpiData)
# 17 SOUNDEX field (EpiData)
#
for (i in 1L:nvars) {
if (numbers[i])
data[[i]] <- as.numeric(data[[i]])
else if (header$type[i] == 5L)
data[[i]] <- ifelse(data[[i]] %in% c("Y", "N"), data[[i]] == "Y", NA)
else if (header$type[i] %in% c(11L, 16L) && header$len[i] == 5L && guess.broken.dates)
data[[i]] <- as.Date(strptime(paste(data[[i]], thisyear, sep = "/"), format = "%d/%m/%Y"))
else if (header$type[i] %in% c(11L, 16L) && header$len[i] == 8L && guess.broken.dates)
data[[i]] <- as.Date(strptime(data[[i]], format = "%d/%m/%y"))
else if (header$type[i] %in% c(11L, 16L) && header$len[i] == 10L)
data[[i]] <- as.Date(strptime(data[[i]], format = "%d/%m/%Y"))
else if (header$type[i] %in% c(2L, 10L) && header$len[i] == 5L && guess.broken.dates)
data[[i]] <- as.Date(strptime(paste(data[[i]], thisyear, sep = "/"), format = "%m/%d/%Y"))
else if (header$type[i] %in% c(2L, 10L) && header$len[i] == 8L && guess.broken.dates)
data[[i]] <- as.Date(strptime(data[[i]], format = "%m/%d/%y"))
else if (header$type[i] %in% c(2L, 10L) && header$len[i] == 10L)
data[[i]] <- as.Date(strptime(data[[i]], format = "%m/%d/%Y"))
#
# SOUNDEX (type 17) fields
#
else if (header$type[i] == 17L) {
data[[i]][substr(data[[i]], 1L, 1L) == " "] <- NA
data[[i]] <- substr(data[[i]], 1L, 5L)
}
else {
blanks <- grep("^[[:blank:]]*$", data[[i]])
data[[i]][blanks] <- NA
}
}
if (!is.na(read.deleted) && read.deleted)
attr(data, "deleted") <- deleted
attr(data, "prompts") <- comments
#
# Added parameter and code to specify lower case variable names
#
if (lower.case.names)
names(data) <- tolower(names(data))
data
}
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