Merge pull request #28 from tscnlab/dev

.Rbuildignore

@@ -15,4 +15,5 @@
 ^vignettes/articles$
 ^\.gitlab-ci\.yml$
 ^cran-comments\.md$
-^LightLogR-manual\.tex$
+^LightLogR-manual\.tex$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.3.8
+Date: 2024-07-04 09:38:13 UTC
+SHA: 8714a0b64b88a425313e7a6c19913fb3878cf1d0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LightLogR
 Title: Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
-Version: 0.3.8
+Version: 0.4.0
 Authors@R: c(
     person("Johannes", "Zauner", 
       email = "johannes.zauner@tum.de", role = c("aut", "cre"),

NAMESPACE

@@ -41,6 +41,7 @@ export(interdaily_stability)
 export(interval2state)
 export(intradaily_variability)
 export(join_datasets)
+export(ll_import_expr)
 export(midpointCE)
 export(nvRC)
 export(nvRC_circadianBias)
@@ -52,6 +53,7 @@ export(period_above_threshold)
 export(pulses_above_threshold)
 export(sc2interval)
 export(sleep_int2Brown)
+export(supported_devices)
 export(symlog_trans)
 export(threshold_for_duration)
 export(timing_above_threshold)

NEWS.md

@@ -1,3 +1,21 @@
+# LightLogR 0.4.0 "Nautical dawn"
+
+* release on CRAN!
+
+* changed the `supported.devices` list to a function `supported_devices()` instead, so the documentation automatically updates with the list of supported devices. Similarly, `ll_import_expr` is now `ll_import_expr()`.
+
+* added support for the Meta `VEET` device for visual experience measurements
+
+* added support for the `Kronowise` device
+
+* added support for the MPI `melanopiQ Circadian Eye` (Prototype)
+
+* rewrote the import function for `Actiwatch_Spectrum`, as the sample file the original was based off, had specific formatting to German standards. Now, the German version can still be called through `Actiwatch_Spectrum_de`, wheras the main function refers to the english/international format.
+
+* updated the landing page for the website with a list of supported devices and a table of metrics
+
+* small changes to documentation
+
 # LightLogR 0.3.8
 
 * Submission to CRAN

R/aaa.r

@@ -7,7 +7,6 @@ empty_function <- function() {
 }
 
 .onLoad <- function(libname, pkgname) {
-  utils::globalVariables("supported.devices")
   utils::globalVariables(".")
 }
 

R/cut_Datetime.R

@@ -12,7 +12,7 @@
 #'   `Datetime.colname`.
 #' @param unit Unit of binning. See [lubridate::round_date()] for examples. The default is `"3 hours"`. 
 #' @param type One of `"round"`(the default), `"ceiling"` or `"floor"`. Setting
-#'   chooses the relevant function from [lubridate].
+#'   chooses the relevant function from \pkg{lubridate}.
 #' @param Datetime.colname column name that contains the datetime. Defaults to
 #'   `"Datetime"` which is automatically correct for data imported with
 #'   [LightLogR]. Expects a `symbol`. Needs to be part of the `dataset`.

R/data.r

@@ -17,32 +17,4 @@
 #'   \item{Id}{A `character` vector indicating whether the data is from the `Participant` or from the `Environment`.}
 #' }
 #' @source <https://www.tscnlab.org>
-"sample.data.environment"
-
-
-#' A vector of all supported devices for import functions
-#'
-#' These are all supported devices where there is a dedicated import function.
-#' Import functions can be called either through [import_Dataset()] with the
-#' respective `device = "device"` argument, or directly, e.g.,
-#' `import$ActLumus()`.
-#'
-#' @format `supported.devices` A character vector, listing all supported devices
-#' \describe{
-#'   \item{suppored.devices}{strings}
-#' }
-"supported.devices"
-
-#' A list of the specific device import functions
-#'
-#' These expressions are used to import and prepare data from specific devices.
-#' The list is made explicit, so that a user, requiring slight changes to the
-#' import functions, (e.g., because a timestamp is formatted differently) can
-#' modify or add to the list. The list can be turned into a fully functional 
-#' import function through `import_adjustment()`.
-#'
-#' @format `ll_import_expr` A list, with specific expressions for each supported device
-#' \describe{
-#'   \item{ll_import_expr}{expressions}
-#' }
-"ll_import_expr"
+"sample.data.environment"

R/filter_Datetime.R

@@ -3,7 +3,7 @@
 #' Filtering a dataset based on Dates or Datetimes may often be necessary prior
 #' to calcuation or visualization. The functions allow for a filtering based on
 #' simple `strings` or `Datetime` scalars, or by specifying a length. They also
-#' support prior [dplyr] grouping, which is useful, e.g., when you only want to
+#' support prior \pkg{dplyr} grouping, which is useful, e.g., when you only want to
 #' filter the first two days of measurement data for every participant,
 #' regardless of the actual date. If you want to filter based on times of the
 #' day, look to [filter_Time()].
@@ -18,10 +18,10 @@
 #' * If `length` is provided and one of start/end is not, the other will be calculated based on the given value.
 #' * If `length` is provided and both of start/end are NULL, the time from the
 #'   respective start is taken.
-#' @param length Either a Period or Duration from [lubridate]. E.g., `days(2) +
+#' @param length Either a Period or Duration from \pkg{lubridate}. E.g., `days(2) +
 #'   hours(12)` will give a period of 2.5 days, whereas `ddays(2) + dhours(12)`
 #'   will give a duration. For the difference between periods and durations look
-#'   at the documentation from [lubridate]. Basically, periods model clocktimes,
+#'   at the documentation from \pkg{lubridate}. Basically, periods model clocktimes,
 #'   whereas durations model physical processes. This matters on several
 #'   occasions, like leap years, or daylight savings. You can also provide a
 #'   `character` scalar in the form of e.g. "1 day", which will be converted

R/gg_day.r

@@ -60,15 +60,15 @@
 #'   function (see examples).
 #' @param x.axis.breaks,y.axis.breaks Where should breaks occur on the x and
 #'   y.axis? Expects a `numeric vector` with all the breaks. If you want to
-#'   activate the default behaviour of [ggplot2], you need to put in
+#'   activate the default behaviour of \pkg{ggplot2}, you need to put in
 #'   [ggplot2::waiver()].
 #' @param y.scale.sc `logical` for whether scientific notation shall be used.
 #'   Defaults to `FALSE`.
 #' @param geom What geom should be used for visualization? Expects a `character`
 #' * `"point"` for [ggplot2::geom_point()]
 #' * `"line"`  for [ggplot2::geom_line()]
 #' * `"ribbon"` for [ggplot2::geom_ribbon()]
-#' * as the value is just input into the `geom_` function from [ggplot2], other variants work as well, but are not extensively tested.
+#' * as the value is just input into the `geom_` function from \pkg{ggplot2}, other variants work as well, but are not extensively tested.
 #' @param group Optional column name that defines separate sets. Useful for
 #'   certain geoms like `boxplot`.Expects anything that works with the layer
 #'   data [ggplot2::aes()]

R/gg_days.R

@@ -21,7 +21,7 @@
 #' @param y.axis.breaks Where should breaks occur on the y.axis? Expects a
 #'   `numeric vector` with all the breaks or a function that calculates them
 #'   based on the limits. If you want to activate the default behaviour of
-#'   [ggplot2], you need to put in [ggplot2::waiver()].
+#'   \pkg{ggplot2}, you need to put in [ggplot2::waiver()].
 #' @param x.axis.breaks The (major) breaks of the x-axis. Defaults to
 #'   [Datetime_breaks()]. The function has several options for adjustment. The
 #'   default setting place a major break every 12 hours, starting at 12:00 of