Dev

.Rbuildignore

@@ -18,4 +18,6 @@
 ^cran-comments\.md$
 ^LightLogR-manual\.tex$
 ^CRAN-SUBMISSION$
-^CODE_OF_CONDUCT\.md$
+^CODE_OF_CONDUCT\.md$
+^\.positai$
+^\.claude$

.gitignore

@@ -38,3 +38,4 @@ docs
 inst/doc
 # DS_Store file
 .DS_Store
+.positai

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: LightLogR
 Title: Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
-Version: 0.10.2
+Version: 0.10.3
 Authors@R: c(
     person("Johannes", "Zauner", 
       email = "johannes.zauner@tum.de", role = c("aut", "cre"),
@@ -12,7 +12,7 @@ Authors@R: c(
       email = "steffen.hartmeyer@epfl.ch", role = "aut",
       comment = c(ORCID = "0000-0002-2813-2668")),
     person("European Partnership on Metrology", role = "fnd", comment = "The project (22NRM05 MeLiDos) has received funding from the European Partnership on Metrology, co-financed by the European Union's Horizon Europe Research and Innovation Programme, EURAMET, and the Participating States. Views and opinions expressed are those of the authors and do not necessarily reflect those of the European Union or EURAMET."),
-    person("Wellcome Trust", role = "fnd", comment = "LightLogR's development is supported by the Wellcome Trust (www.wellcome.org), 226787/2/22/Z."),
+    person("Wellcome Trust", role = "fnd", comment = c("LightLogR's development is supported by the Wellcome Trust (wellcome.org), 226787/2/22/Z.")),
     person("Reality Labs Research", role = "fnd", comment = "LightLogR's development is supported by the GLEE project (Global Light Exposure Engine, www.visualdiet.org) funded by Reality Labs Research."),    
     person("Translational Sensory and Circadian Neuroscience Unit (MPS/TUM/TUMCREATE)", comment = c(URL = "www.tscnlab.org"), role = "cph"))
 Description: Import, processing, validation, and visualization of personal light exposure measurement data from wearable devices. The package implements features such as the import of data and metadata files, conversion of common file formats, validation of light logging data, verification of crucial metadata, calculation of common parameters, and semi-automated analysis and visualization.

NEWS.md

@@ -1,3 +1,7 @@
+# LightLogR 0.10.3
+
+* `LYS` import now works with any timestamp column in raw data, as long as it starts with `timestamp`
+
 # LightLogR 0.10.2
 
 * `add_states()` no longer creates duplicate observations at identical start/endpoints. The default behavior is now that the `start` is inclusive and `end` is exclusive. Adjust the new `bounds` argument for more options.

R/gg_state.R

@@ -69,24 +69,13 @@
 #'  ggplot2::scale_fill_manual(values=c("#868686FF", "#EFC000FF", "#0073C2FF"))
 #'  #this line is simply for sensible colors
 #'
-#' #same, but with gg_day()
-#' state_data |>
-#'  dplyr::filter(Id == "Participant") |>
-#'  gg_day(geom = "line") |>
-#'  gg_states(state, fill = "red")
 #'
 #'  #more complex state
 #'  state_data |>
 #'  dplyr::filter(Id == "Participant") |>
 #'  gg_day(geom = "line") |>
 #'  gg_states(state2, aes_fill = state2)
 #'
-#'  #with gg_doubleplot
-#'  state_data |>
-#'  dplyr::filter(Id == "Participant") |>
-#'  gg_doubleplot() |>
-#'  gg_states(state2, aes_fill = state2)
-#'
 #'  #setting the height of the bars 
 #'  state_data |>
 #'  dplyr::filter(Id == "Participant") |>

R/import_expressions.R

@@ -181,7 +181,7 @@ import_expr <- list(
                       ...
       ))
     data <- data %>%
-      dplyr::rename(Datetime = timestamp,
+      dplyr::rename(Datetime = starts_with("timestamp"),
                     MEDI = mEDI) %>%
       dplyr::mutate(Datetime =
                       Datetime %>% lubridate::dmy_hms() %>% 

README.md

@@ -96,7 +96,9 @@ library(LightLogR)
 #the following packages are needed for the examples as shown below.
 library(flextable)
 library(dplyr)
+#> Warning: package 'dplyr' was built under R version 4.5.2
 library(ggplot2)
+#> Warning: package 'ggplot2' was built under R version 4.5.2
 ```
 
 ### Import
@@ -109,10 +111,10 @@ filename <-
   system.file("extdata/205_actlumus_Log_1020_20230904101707532.txt.zip", 
               package = "LightLogR")
 dataset <- import$ActLumus(filename, "Europe/Berlin", manual.id = "P1")
-#> Multiple files in zip: reading '205_actlumus_Log_1020_20230904101707532.txt'
 #> 
 #> Successfully read in 61'016 observations across 1 Ids from 1 ActLumus-file(s).
 #> Timezone set is Europe/Berlin.
+#> The system timezone is Europe/Madrid. Please correct if necessary!
 #> 
 #> First Observation: 2023-08-28 08:47:54
 #> Last Observation: 2023-09-04 10:17:04
@@ -180,6 +182,10 @@ dataset |>
   geom_line(col = "red", linewidth = 0.25) + 
   labs(title = "Personal light exposure across a week", 
        subtitle = "Boxplot in 3-hour bins")
+#> Warning: Orientation is not uniquely specified when both the x and y aesthetics are
+#> continuous. Picking default orientation 'x'.
+#> Orientation is not uniquely specified when both the x and y aesthetics are
+#> continuous. Picking default orientation 'x'.
 ```
 
 <img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
@@ -451,8 +457,6 @@ At present, these are the devices we support in LightLogR:
 
 - Actiwatch_Spectrum
 
-- Actiwatch_Spectrum_de
-
 - ActLumus
 
 - ActTrust
@@ -540,14 +544,11 @@ repository](https://github.com/tscnlab/LightLogR/issues).
 ## About the creation and funding of LightLogR
 
 **LightLogR** is developed by the [*Translational Sensory & Circadian
-Neuroscience*](https://www.tscnlab.org) lab, a joint group from the
-[Technical University of Munich](https://www.tum.de/en/) and the [Max
-Planck Institute for Biological Neuroscience Unit
-(MPS/TUM/TUMCREATE)\*](https://www.tscnlab.org), a joint group based at
-the [Technical University of Munich](https://www.tum.de/en/),
-[TUMCREATE](https://www.tum-create.edu.sg/), the [Max Planck Institute
-for Biological
-Cybernetics](https://www.mpg.de/152075/biological-cybernetics).
+Neuroscience Unit (MPS/TUM/TUMCREATE*](https://www.tscnlab.org), a joint
+group based at the [Max Planck Institute for Biological
+Cybernetics](https://www.mpg.de/152075/biological-cybernetics), the
+[Technical University of Munich](https://www.tum.de/en/), and
+[TUMCREATE](https://www.tum-create.edu.sg/), .
 
 [*MeLiDos*](https://www.melidos.eu) is a joint,
 [EURAMET](https://www.euramet.org)-funded project involving sixteen

cran-comments.md

@@ -1,3 +1,9 @@
+## Submission Version 0.10.3
+
+### R CMD check results
+
+0 errors ✔ | 0 warnings ✔ | 0 notes ✔
+
 ## Submission Version 0.10.0
 
 ### R CMD check results