Merge branch 'feat@time-to-posix-and-character' into dev

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: naryn
 Title: Native Access Medical Record Retriever for High Yield Analytics
-Version: 2.6.25
+Version: 2.6.26
 Authors@R: c(
     person("Misha", "Hoichman", , "[email protected]", role = "aut"),
     person("Aviezer", "Lifshitz", , "[email protected]", role = c("aut", "cre")),

NAMESPACE

@@ -9,6 +9,7 @@ export(.naryn)
 export(day)
 export(days)
 export(emr_annotate)
+export(emr_char2time)
 export(emr_cor)
 export(emr_date2time)
 export(emr_db.connect)
@@ -47,14 +48,17 @@ export(emr_filters.info)
 export(emr_ids_coverage)
 export(emr_ids_vals_coverage)
 export(emr_monthly_iterator)
+export(emr_posix2time)
 export(emr_quantiles)
 export(emr_screen)
 export(emr_summary)
 export(emr_time)
+export(emr_time2char)
 export(emr_time2date)
 export(emr_time2dayofmonth)
 export(emr_time2hour)
 export(emr_time2month)
+export(emr_time2posix)
 export(emr_time2year)
 export(emr_track.addto)
 export(emr_track.attr.export)

NEWS.md

@@ -1,3 +1,7 @@
+# naryn 2.6.26 
+
+* Added `emr_time2posix`, `emr_posix2time`,  `emr_time2char` and `emr_char2time` functions.
+
 # naryn 2.6.25
 
 * Fixed clang warnings.

R/time.R

@@ -198,6 +198,93 @@ emr_time2date <- function(time) {
     )
 }
 
+#' Convert EMR time to POSIXct
+#'
+#' These function converts EMR time to POSIXct format. It takes the EMR time as input and returns the corresponding POSIXct object.
+#'
+#' @param time The EMR time to be converted.
+#' @param show_hour Logical value indicating whether to include the hour in the output. Default is FALSE.
+#' @param tz Time zone to be used for the output POSIXct object. Default is "UTC".
+#' @param posix A POSIXct object to be converted to EMR time.
+#'
+#' @return A POSIXct object representing the converted time.
+#'
+#' @examples
+#' # 30 January, 1938, 6:00 - birthday of Islam Karimov
+#' t1 <- emr_date2time(30, 1, 1938, 6)
+#' # September 2, 2016, 7:00 - death of Islam Karimov
+#' t2 <- emr_date2time(2, 9, 2016, 7)
+#'
+#' emr_time2posix(c(t1, t2))
+#' emr_time2posix(c(t1, t2), show_hour = TRUE)
+#'
+#' emr_posix2time(emr_time2posix(c(t1, t2), show_hour = TRUE))
+#'
+#' # Note that when show_hour = FALSE, the hour is set to 0
+#' # and therefore the results would be different from the original time values
+#' emr_posix2time(emr_time2posix(c(t1, t2)))
+#'
+#' @export
+emr_time2posix <- function(time, show_hour = FALSE, tz = "UTC") {
+    year <- emr_time2year(time)
+    month <- emr_time2month(time)
+    day <- emr_time2dayofmonth(time)
+
+    if (show_hour) {
+        hour <- emr_time2hour(time)
+        return(as.POSIXct(paste(year, month, day, hour, sep = "-"), format = "%Y-%m-%d-%H", tz = tz))
+    }
+
+    return(as.POSIXct(paste(year, month, day, sep = "-"), format = "%Y-%m-%d", tz = tz))
+}
+
+#' Convert time to character format
+#'
+#' This function converts a given time value to a character format in the form of "%Y-%m-%d" or "%Y-%m-%d %H:%M:%S" depending on the value of the `show_hour` parameter.
+#'
+#' @param time The time value to be converted.
+#' @param show_hour Logical value indicating whether to include the hour in the output. Default is FALSE.
+#' @param char A character string to be converted to EMR time.
+#'
+#' @return A character string representing the converted time value.
+#'
+#' @examples
+#' # 30 January, 1938, 6:00 - birthday of Islam Karimov
+#' t1 <- emr_date2time(30, 1, 1938, 6)
+#' # September 2, 2016, 7:00 - death of Islam Karimov
+#' t2 <- emr_date2time(2, 9, 2016, 7)
+#'
+#' emr_time2char(c(t1, t2))
+#' emr_time2char(c(t1, t2), show_hour = TRUE)
+#'
+#' emr_char2time(emr_time2char(c(t1, t2), show_hour = TRUE))
+#'
+#' # Note that when show_hour = FALSE, the hour is set to 0
+#' # and therefore the results would be different from the original time values
+#' emr_char2time(emr_time2char(c(t1, t2)))
+#'
+#' @export
+emr_time2char <- function(time, show_hour = FALSE) {
+    as.character(emr_time2posix(time, show_hour = show_hour))
+}
+
+#' @rdname emr_time2posix
+#' @export
+emr_posix2time <- function(posix) {
+    day <- as.numeric(format(posix, "%d"))
+    month <- as.numeric(format(posix, "%m"))
+    year <- as.numeric(format(posix, "%Y"))
+    hour <- as.numeric(format(posix, "%H"))
+
+    return(emr_date2time(day, month, year, hour))
+}
+
+#' @rdname emr_time2char
+#' @export
+emr_char2time <- function(char) {
+    return(emr_posix2time(as.POSIXct(char)))
+}
+
 #' Convert time periods to internal time format
 #'
 #' Convert time periods to internal time format

tests/testthat/test-date2time.R

@@ -211,3 +211,57 @@ test_that("periodic iterators fail when not given etime and n", {
     expect_error(emr_monthly_iterator(emr_date2time(1, 1, 2002)))
     expect_error(emr_yearly_iterator(emr_date2time(1, 1, 2002)))
 })
+
+test_that("emr_time2posix returns correct POSIXct object without hour", {
+    time <- emr_date2time(30, 1, 1938, 6)
+    expected <- as.POSIXct("1938-01-30", format = "%Y-%m-%d", tz = "UTC")
+    result <- emr_time2posix(time, show_hour = FALSE)
+    expect_equal(result, expected)
+})
+
+test_that("emr_time2posix returns correct POSIXct object with hour", {
+    time <- emr_date2time(30, 1, 1938, 6)
+    expected <- as.POSIXct("1938-01-30 06:00:00", format = "%Y-%m-%d %H:%M:%S", tz = "UTC")
+    result <- emr_time2posix(time, show_hour = TRUE)
+    expect_equal(result, expected)
+})
+
+test_that("emr_time2char returns correct character string without hour", {
+    time <- emr_date2time(30, 1, 1938, 6)
+    expected <- "1938-01-30"
+    result <- emr_time2char(time, show_hour = FALSE)
+    expect_equal(result, expected)
+})
+
+test_that("emr_time2char returns correct character string with hour", {
+    time <- emr_date2time(30, 1, 1938, 6)
+    expected <- "1938-01-30 06:00:00"
+    result <- emr_time2char(time, show_hour = TRUE)
+    expect_equal(result, expected)
+})
+
+# Test emr_time2posix function
+test_that("emr_time2posix converts EMR time to POSIXct", {
+    # Test case 1: EMR time with hour
+    time1 <- emr_date2time(30, 1, 1938, 6)
+    expected1 <- as.POSIXct("1938-01-30 06:00:00", tz = "UTC")
+    expect_equal(emr_time2posix(time1, show_hour = TRUE), expected1)
+
+    # Test case 2: EMR time without hour
+    time2 <- emr_date2time(2, 9, 2016, 0)
+    expected2 <- as.POSIXct("2016-09-02", tz = "UTC")
+    expect_equal(emr_time2posix(time2, show_hour = FALSE), expected2)
+})
+
+# Test emr_time2char function
+test_that("emr_time2char converts time to character format", {
+    # Test case 1: Time with hour
+    time1 <- emr_date2time(30, 1, 1938, 6)
+    expected1 <- "1938-01-30 06:00:00"
+    expect_equal(emr_time2char(time1, show_hour = TRUE), expected1)
+
+    # Test case 2: Time without hour
+    time2 <- emr_date2time(2, 9, 2016, 0)
+    expected2 <- "2016-09-02"
+    expect_equal(emr_time2char(time2, show_hour = FALSE), expected2)
+})