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#' Read data table files containing count values
#'
#' @param file A character scalar giving path to an automatically-generated csv
#' file with count values
#' @param verbose A logical scalar: Print processing updates?
#' @param header A logical scalar: Are variable names contained in first row of
#' file?
#' @param header_timestamp_format character. Space delimited format of the date
#' and time in the file header (default is \code{\%m/\%d/\%Y \%H:\%M:\%S})
#' @param ... Further arguments passed to \code{data.table::fread}
#'
#' @return A data frame reflecting the data contained in the csv file
#' @export
#'
#' @examples
#' AG_counts <- read_AG_counts(
#' system.file(
#' "extdata",
#' "example1sec.csv",
#' package = "AGread"
#' ),
#' header = TRUE
#' )
#' head(AG_counts)
#'
read_AG_counts <- function(
file, verbose = FALSE, header = FALSE,
header_timestamp_format = "%m/%d/%Y %H:%M:%S", ...
) {
timer <- PAutilities::manage_procedure(
"Start", "\nReading", basename(file), verbose = verbose
)
# Get metadata
if (verbose) message_update(1, file = file)
meta <- AG_meta(file, verbose, header_timestamp_format)
file_mode <-
(modes$mode == meta$mode) %>%
modes[., ] %T>%
{stopifnot(nrow(.) == 1)}
# Pick out expected variable names
mode_vars <-
names(file_mode) %>%
sapply(function(x) file_mode[ ,x] == "X") %>%
{names(.)[.]}
variables <-
sapply(
mode_vars, AG_col_names,
simplify = FALSE, USE.NAMES = FALSE
) %>%
do.call(c, .)
# Read the file
if (verbose) message_update(5)
AG <-
data.table::fread(
file,
stringsAsFactors = FALSE,
header = header,
skip = find_skip(file),
...
) %>%
data.frame(stringsAsFactors = FALSE, row.names = NULL)
# Deal with mis-reading case
if (all(sapply(AG, class) %in% c("character", "factor"))) {
message_update(14, TRUE)
return(AG)
}
# Check for date/time variables
time_vars <- sapply(AG[ ,1:2], function(x) {
is.character(x) & any(grepl("[/:]", x))
})
if (all(time_vars)) {
if (verbose) message_update(8)
mode_vars <- append(
mode_vars, c("Date", "Time"), 0
)
variables <- append(
variables, c("Date", "Time"), 0
)
first_col <- 3
} else {
first_col <- 1
}
# Check for vector magnitude
if (verbose) cat("\n......Checking for vector magnitude")
vm_test <-
get_VM_C(AG[ ,first_col], AG[ ,first_col+1], AG[ ,first_col+2]) %>%
round(2) %>%
all.equal(AG[ ,ncol(AG)], tolerance = 0.015) %>%
isTRUE(.)
if (vm_test & (!"Vector.Magnitude" %in% variables)) {
mode_vars <- append(mode_vars, "Vector.Magnitude")
variables <- append(variables, "Vector.Magnitude")
}
# Deal with the automatic-naming case for dummy-coded inclinometer
if (length(variables) == ncol(AG)) {
if (verbose) {
message_update(2)
}
names(AG) <- variables
AG <- AG_time(AG, meta)
if (verbose) message_update(
16, dur = PAutilities::get_duration(timer)
)
return(AG)
}
# Deal with the automatic-naming case for discrete (0-3) inclinometer
if (length(mode_vars) == ncol(AG)) {
if (verbose) message_update(28)
names(AG) <- capitalize(mode_vars)
AG <- AG_time(AG, meta)
if (verbose) message_update(16, dur = PAutilities::get_duration(timer))
return(AG)
}
# Deal with cases not caught in previous cases
if (!"V1" %in% names(AG)) {
if (verbose) message_update(3)
AG <- AG_time(AG, meta)
if (verbose) message_update(
16, dur = PAutilities::get_duration(timer)
)
return(AG)
} else {
stop(
"File reading failed for ",
basename(file), ".",
" \n Consider submitting a bug report",
" (see `packageDescription(\"AGread\")`).",
call. = FALSE
)
}
}
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