Merge pull request #25 from tscnlab/dev

added tests and small aspects to articles
tscnlab · Jul 3, 2024 · f3523e2 · f3523e2
2 parents f6a6c59 + 9152ab3
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,5 @@
 ^app\.R$
 ^vignettes/articles$
 ^\.gitlab-ci\.yml$
+^cran-comments\.md$
+^LightLogR-manual\.tex$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: LightLogR
-Title: Work With Data from Wearable Light Loggers and Optical Radiation Dosimeters
-Version: 0.3.7
+Title: Process Data from Wearable Light Loggers and Optical Radiation Dosimeters
+Version: 0.3.8
 Authors@R: c(
     person("Johannes", "Zauner", 
       email = "[email protected]", role = c("aut", "cre"),
@@ -15,17 +15,11 @@ Authors@R: c(
     person("EURAMET", role = "fnd", comment = "European Association of National Metrology Institutes. Website: www.euramet.org. Grant Number: 22NRM05 MeLiDos. Grant Statement: The project (22NRM05 MeLiDos) has received funding from the European Partnership on Metrology, co-financed from the European Union’s Horizon Europe Research and Innovation Programme and by the Participating States."),    
     person("European Union", role = "fnd", comment = "Co-funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or EURAMET. Neither the European Union nor the granting authority can be held responsible for them."),
     person("TSCN-Lab", comment = c(URL = "www.tscnlab.org"), role = "cph"))
-Description: LightLogR is a package under development as part of the MeLiDos 
-    project aimed at developing a standard workflow for wearable light logger 
-    data and optical radiation dosimeters. MeLiDos is a joint, EURAMET-funded 
-    project involving sixteen partners across Europe. Its primary contributions 
-    towards fostering FAIR data include the development of a common file format, 
-    robust metadata descriptors, and an accompanying open-source software 
-    ecosystem.
+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.
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://github.com/tscnlab/LightLogR,
     https://tscnlab.github.io/LightLogR/,
     https://zenodo.org/doi/10.5281/zenodo.11562600
@@ -67,4 +61,3 @@ Suggests:
     testthat (>= 3.0.0),
     tidyverse
 Config/testthat/edition: 3
-VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# LightLogR 0.3.8
+
+* Submission to CRAN
+
 # LightLogR 0.3.7 "Astronomical dawn"
 
 * Changes to the tutorial articles on the website

diff --git a/R/import_LL.R b/R/import_LL.R
@@ -66,28 +66,56 @@
 #' ```
 #' 
 #'   ## ActLumus 
+#'   Manufacturer: Condor Instruments
+#'   Model: ActLumus
+#'   Implemented: 2023
 #'   A sample file is provided with the package, it can be accessed through
 #'   `system.file("extdata/205_actlumus_Log_1020_20230904101707532.txt.zip",
 #'   package = "LightLogR")`. It does not need to be unzipped to be imported.
 #'   This sample file is a good example for a regular dataset without gaps
-#'   ## LYS 
+#'   ## LYS
+#'   Manufacturer: LYS Technologies
+#'   Model: LYS Button
+#'   Implemented: 2023
 #'   A sample file is provided with the package, it can be accessed
 #'   through `system.file("extdata/sample_data_LYS.csv", package =
 #'   "LightLogR")`. This sample file is a good example for an irregular dataset.
 #'   ## Actiwatch_Spectrum
+#'   Manufacturer: Philips Respironics
+#'   Model: Actiwatch Spectrum
+#'   Implemented: 2023
 #'   **Required Argument: `column_names`** A character vector containing column 
 #'   names in the order in which they appear in the file. This is necessary to 
 #'   find the starting point of actual data.
 #'   ## ActTrust
+#'   Manufacturer: Condor Instruments
+#'   Model: ActTrust1, ActTrust2
+#'   Implemented: 2024
 #'   This function works for both ActTrust 1 and 2 devices
 #'   ## Speccy
-#'   .  
+#'   Manufacturer: Monash University
+#'   Model: Speccy
+#'   Implemented: 2024
 #'   ## DeLux
-#'   . 
+#'   Manufacturer: Intelligent Automation Inc
+#'   Model: DeLux
+#'   Implemented: 2023
 #'   ## LiDo
-#'   .  
+#'   Manufacturer: University of Lucerne
+#'   Model: LiDo
+#'   Implemented: 2023
 #'   ## SpectraWear
-#'   .
+#'   Manufacturer:
+#'   Model: SpectraWear
+#'   Implemented: 2024
+#'   ## NanoLambda
+#'   Manufacturer: NanoLambda
+#'   Model: XL-500 BLE
+#'   Implemented: 2024
+#'   ## LightWatcher
+#'   Manufacturer: Object-Tracker
+#'   Model: LightWatcher
+#'   Implemented: 2024
 #'
 #' @section Examples:
 #'

diff --git a/R/metric_EMA.R b/R/metric_EMA.R
@@ -30,11 +30,11 @@
 #' @references 
 #'    Price, L. L. A. (2014). On the Role of Exponential Smoothing in Circadian 
 #'    Dosimetry. \emph{Photochemistry and Photobiology}, 90(5), 1184-1192.
-#'    \url{https://doi.org/10.1111/php.12282}
+#'    \doi{10.1111/php.12282}
 #'    
 #'    Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'    Quantification metrics. \emph{Lighting Research & Technology}. 
-#'    \url{https://doi.org/10.1177/14771535231170500}
+#'    \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #' sample.data.environment.EMA = sample.data.environment %>%

diff --git a/R/metric_barroso.R b/R/metric_barroso.R
@@ -48,11 +48,11 @@
 #' @references 
 #'    Barroso, A., Simons, K., & Jager, P. de. (2014). Metrics of circadian 
 #'    lighting for clinical investigations. \emph{Lighting Research & Technology},
-#'    46(6), 637–649. \url{https://doi.org/10.1177/1477153513502664}
+#'    46(6), 637–649. \doi{10.1177/1477153513502664}
 #'    
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #' 

diff --git a/R/metric_bright_dark_period.R b/R/metric_bright_dark_period.R
@@ -38,7 +38,7 @@
 #' @references 
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @export
 #' 

diff --git a/R/metric_centroidLE.R b/R/metric_centroidLE.R
@@ -25,11 +25,11 @@
 #'    L. K., Picard, R. W., Lockley, S. W., Klerman, E. B., & Czeisler, C. A. (2017).
 #'    Irregular sleep/wake patterns are associated with poorer academic performance
 #'    and delayed circadian and sleep/wake timing. \emph{Scientific Reports},
-#'    7(1), 3216. \url{https://doi.org/10.1038/s41598-017-03171-4}
+#'    7(1), 3216. \doi{10.1038/s41598-017-03171-4}
 #'    
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #' # Dataset with POSIXct time vector

diff --git a/R/metric_disparity_index.R b/R/metric_disparity_index.R
@@ -20,11 +20,11 @@
 #'   Martín-Vide, J., & Peñuelas, J. (2018).
 #'   The consecutive disparity index, D: A measure of temporal variability in
 #'   ecological studies. \emph{Ecosphere}, 9(12), e02527.
-#'   \url{https://doi.org/10.1002/ecs2.2527}
+#'   \doi{10.1002/ecs2.2527}
 #'   
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #' dataset1 <-

diff --git a/R/metric_duration_above_threshold.R b/R/metric_duration_above_threshold.R
@@ -27,7 +27,7 @@
 #' @references 
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @export
 #' 

diff --git a/R/metric_frequency_crossing_threshold.R b/R/metric_frequency_crossing_threshold.R
@@ -19,11 +19,11 @@
 #' @references 
 #'    Alvarez, A. A., & Wildsoet, C. F. (2013). Quantifying light
 #'    exposure patterns in young adult students. \emph{Journal of Modern Optics},
-#'    60(14), 1200–1208. \url{https://doi.org/10.1080/09500340.2013.845700}
+#'    60(14), 1200–1208. \doi{10.1080/09500340.2013.845700}
 #'    
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 # 

diff --git a/R/metric_interdaily_stability.R b/R/metric_interdaily_stability.R
@@ -24,11 +24,11 @@
 #'    McCall, W. V., & Rosenquist, P. B. (1999). Bright Light Therapy: Improved
 #'    Sensitivity to Its Effects on Rest-Activity Rhythms in Alzheimer Patients
 #'    by Application of Nonparametric Methods. \emph{Chronobiology International},
-#'    16(4), 505–518. \url{https://doi.org/10.3109/07420529908998724}
+#'    16(4), 505–518. \doi{10.3109/07420529908998724}
 #'    
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #'

diff --git a/R/metric_intradaily_variability.R b/R/metric_intradaily_variability.R
@@ -22,11 +22,11 @@
 #'    McCall, W. V., & Rosenquist, P. B. (1999). Bright Light Therapy: Improved
 #'    Sensitivity to Its Effects on Rest-Activity Rhythms in Alzheimer Patients
 #'    by Application of Nonparametric Methods. \emph{Chronobiology International},
-#'    16(4), 505–518. \url{https://doi.org/10.3109/07420529908998724}
+#'    16(4), 505–518. \doi{10.3109/07420529908998724}
 #'    
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 #'

diff --git a/R/metric_midpointCE.R b/R/metric_midpointCE.R
@@ -22,11 +22,11 @@
 #'   Shochat, T., Santhi, N., Herer, P., Flavell, S. A., Skeldon, A. C.,
 #'   & Dijk, D.-J. (2019). Sleep Timing in Late Autumn and Late Spring Associates
 #'   With Light Exposure Rather Than Sun Time in College Students.
-#'   \emph{Frontiers in Neuroscience}, 13. \url{https://doi.org/10.3389/fnins.2019.00882}
+#'   \emph{Frontiers in Neuroscience}, 13. \doi{10.3389/fnins.2019.00882}
 #'   
 #'   Hartmeyer, S.L., Andersen, M. (2023). Towards a framework for light-dosimetry studies:
 #'   Quantification metrics. \emph{Lighting Research & Technology}. 
-#'   \url{https://doi.org/10.1177/14771535231170500}
+#'   \doi{10.1177/14771535231170500}
 #'
 #' @examples
 # Dataset with POSIXct time vector