Dev

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.6.26
-Date: 2024-01-14 19:09:33 UTC
-SHA: 2c56e06dccf3c5d22dbbd12e4dc746887ff0c28a
+Version: 2.6.30
+Date: 2024-09-27 08:34:48 UTC
+SHA: f465f7137992d8df2e04d2dfa10365e421076390

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: naryn
 Title: Native Access Medical Record Retriever for High Yield Analytics
-Version: 2.6.26
+Version: 2.6.30
 Authors@R: c(
     person("Misha", "Hoichman", , "[email protected]", role = "aut"),
     person("Aviezer", "Lifshitz", , "[email protected]", role = c("aut", "cre")),
@@ -54,4 +54,4 @@ Language: en-US
 LazyLoad: yes
 NeedsCompilation: yes
 OS_type: unix
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

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

@@ -1,5 +1,23 @@
+# naryn 2.6.30 
+
+* Removed non-API calls to R in the C++ code.
+
+# naryn 2.6.29 
+
+* Fixed *noRemap* additional issue by adding `Rf_` prefix in the c++ code.
+
+# naryn 2.6.28 
+
+* Fix: `emr_track.mv` did not move track attributes. 
+* "exists" virtual track function without parameters now checks for existence of any value.
+
+# naryn 2.6.27
+
+* Fix: do not truncate expression names in `emr_extract` when `tidy=TRUE`.
+
 # naryn 2.6.26 
 
+* Added `emr_time2posix`, `emr_posix2time`,  `emr_time2char` and `emr_char2time` functions.
 * Fixed compilation warnings on M1 Mac.
 
 # naryn 2.6.25

R/naryn-package.R

@@ -13,6 +13,5 @@
 #' @useDynLib naryn emr_dbinit emr_dbreload emr_dbunload emr_db_subset emr_db_subset_ids emr_db_subset_info emr_covariance emr_ids_dist emr_ids_dist_with_iterator emr_ids_vals_dist emr_check_named_filter emr_check_filter_attr_src emr_check_filter_attr_time_shift emr_check_filter_attr_expiration update_logical_tracks_file emr_create_logical emr_remove_logical emr_is_logical emr_logical_track_info emr_ltrack_dependencies emr_get_tracks_attrs update_tracks_attrs_file emr_set_track_attr emr_track_create emr_track_exists emr_logical_track_exists emr_logical_track_names emr_track_db_names emr_track_ids emr_import emr_logical_track_user_info emr_track_info emr_track_names emr_track_mv emr_track_percentile emr_track_rm emr_track_unique emr_check_vtrack emr_check_vtrack_attr_src emr_check_vtrack_attr_func emr_check_vtrack_attr_time_shift emr_check_vtrack_attr_id_map emr_check_vtrack_attr_filter
 #' @useDynLib naryn C_emr_dist C_emr_extract C_emr_quantiles C_emr_screen C_emr_summary C_emr_time2hour C_emr_time2dayofmonth C_emr_time2month C_emr_time2year C_emr_date2time C_emr_annotate
 #' @aliases naryn-package naryn
-#' @docType package
 #' @keywords package
-NULL
+"_PACKAGE"

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

R/track-attributes.R

@@ -83,8 +83,6 @@ emr_track.attr.export <- function(track = NULL, attr = NULL, include_missing = F
     return(res)
 }
 
-
-
 #' Returns the value of the track attribute
 #'
 #' Returns the value of the track attribute.

R/track.R

@@ -670,6 +670,8 @@ emr_track.mv <- function(src, tgt, space = NULL) {
         stop(sprintf("Filter %s already exists", tgt), call. = FALSE)
     }
 
+    attrs <- emr_track.attr.export(src)
+
     if (emr_track.logical.exists(src)) {
         ltrack <- emr_track.logical.info(src)
         emr_track.logical.rm(src, force = TRUE)
@@ -702,6 +704,13 @@ emr_track.mv <- function(src, tgt, space = NULL) {
     if (file.exists(dirname2)) {
         .emr_dir.mv(dirname2, .emr_track.pyvar.dir(tgt))
     }
+
+    # if track has atributes - move them as well
+    if (nrow(attrs) > 0) {
+        purrr::walk2(attrs$attr, attrs$value, ~ {
+            emr_track.attr.set(tgt, .x, .y)
+        })
+    }
 }
 
 

R/vtrack.R

@@ -276,8 +276,8 @@ emr_vtrack.create_from_name <- function(vtrack_name) {
 #' CATEGORICAL DATA SOURCE
 #'
 #' \tabular{lll}{ FUNC \tab PARAM \tab DESCRIPTION \cr value \tab vals/NULL
-#' \tab A source value or -1 if there is more than one. \cr exists \tab vals
-#' \tab 1 if any of the 'vals' exist otherwise 0. \cr sample \tab NULL \tab
+#' \tab A source value or -1 if there is more than one. \cr exists \tab vals/NULL
+#' \tab 1 if any of the 'vals' exist otherwise 0. NULL indicates the existence of any value\cr sample \tab NULL \tab
 #' Uniformly sampled source value. \cr sample.time \tab NULL \tab Time of the
 #' uniformly sampled source value. \cr frequent \tab vals/NULL \tab The most
 #' frequent source value or -1 if there is more than one value. \cr size \tab

cran-comments.md

@@ -2,4 +2,4 @@
 
 0 errors | 0 warnings | 0 notes
 
-* Fixed compilation warnings on M1 Mac.
+* Removed non-API calls to R: 'PRENV', 'PRVALUE', 'R_PromiseExpr'. 

inst/WORDLIST

@@ -14,10 +14,11 @@ MAXTIME
 MINID
 MINTIME
 Makevars
+Mendelson
 NA's
-NaN
 PARAM
 PKGDIR
+POSIXct
 Postmyocardial
 Pre
 Prefetch
@@ -68,6 +69,7 @@ mylist
 naryndb
 ndarray
 ness
+noRemap
 numpy
 param
 params