License changes + paper

.github/workflows/draft_pdf.yml

@@ -0,0 +1,26 @@
+name: Draft PDF
+on: 
+  push:
+  workflow_dispatch:
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

DESCRIPTION

@@ -16,7 +16,7 @@ Authors@R: c(
     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: 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)
+License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: LightLogR authors

NEWS.md

@@ -1,5 +1,7 @@
 # LightLogR 0.4.2
 
+* updated the license to MIT: LightLogR is now permissively licensed
+
 * `import` functions will now give a warning message about identical observations in the provided data files, stop the import process and return a tibble with the duplicate rows. Through the `remove_duplicates` parameter, the user can decide to automatically remove these duplicates during import. **Note: identical observations refers to identical rows when disregarding the filename.**
 
 # LightLogR 0.4.1

paper/paper.bib

@@ -0,0 +1,180 @@
+@article{biller2024,
+    author = {Biller, Anna M. and Fatima, Nayab and Hamberger, Chrysanth and Hainke, Laura and Plankl, Verena and Nadeem, Amna and Kramer, Achim and Hecht, Martin and Spitschan, Manuel},
+    title = {The Ecology of Human Sleep (EcoSleep) Cohort Study: Protocol for a longitudinal repeated measurement burst design study to assess the relationship between sleep determinants and outcomes under real-world conditions across time of year},
+    journal = {Journal of Sleep Research},
+    pages = {e14225},
+    year = {2024},
+    doi = {10.1111/jsr.14225},
+    url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jsr.14225},
+    eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/jsr.14225},
+    keywords = {individual sleep differences, naturalistic conditions, photoperiod, prospective cohort study, season, sleep architecture, sleep variability},
+}
+
+@misc{cran,
+	author = {{Zauner}, {Johannes} and {Hartmeyer}, Steffen L. and {Spitschan}, {Manuel}},
+	title = {{L}ight{L}og{R}: {P}rocess {D}ata from {W}earable {L}ight {L}oggers and {O}ptical {R}adiation {D}osimeters. CRAN Package},
+	howpublished = {\url{https://doi.org/10.32614/CRAN.package.LightLogR}},
+	year = {2024},
+	note = {[Accessed 07-10-2024]},
+}
+
+@article{devries2024,
+    author = {de Vries, SW and Gkaintatzi-Masouti, M and van Duijnhoven, J and Mardaljevic, J and Aarts, MPJ},
+    title = {Recommendations for light-dosimetry field studies based on a meta-analysis of personal light levels of office workers},
+    journal = {Lighting Research \& Technology},
+    volume = {55},
+    pages = {14771535241248540},
+    doi = {10.1177/14771535241248540},
+    month = {May},
+    year = {2024}
+}
+
+@misc{documentation,
+	author = {{Zauner}, {Johannes} and {Hartmeyer}, Steffen L. and {Spitschan}, {Manuel}},
+	title = {{L}ight{L}og{R}: {P}rocess {D}ata from {W}earable {L}ight {L}oggers and {O}ptical {R}adiation {D}osimeters. {D}ocumentation and Tutorials},
+	howpublished = {\url{https://tscnlab.github.io/LightLogR/index.html}},
+	year = {2023},
+	note = {[Accessed 07-10-2024]},
+}
+
+@article{guidolin2024,
+    author = {Guidolin, Carolina and Aerts, Sam and Agbeshie, Gabriel Kwaku and Akuffo, Kwadwo Owusu and Aydin, Sema Nur and Baeza Moyano, David and Bolte, John and Broszio, Kai and Cantarero-Garc{\'\i}a, Guadalupe and Didikoglu, Altug and Gonz{\'a}lez-Lezcano, Roberto Alonso and Joosten-Ma, Hongli and Melero-Tur, Sofia and Nilsson Tengelin, Maria and P{\'e}rez Guti{\'e}rrez, Mar{\'\i}a Concepci{\'o}n and Stefani, Oliver and Svensson, Ingemar and Udovicic, Ljiljana and Zauner, Johannes and Spitschan, Manuel},
+    title = {Protocol for a prospective, multicentre, cross-sectional cohort study to assess personal light exposure [preprint]},
+    journal = {medRxiv},
+    year = {2024},
+    elocation-id = {2024.02.11.24302663},
+    doi = {10.1101/2024.02.11.24302663},
+}
+
+@article{hartmeyer2023,
+    author = {Hartmeyer, S. L. and Webler, F. S. and Andersen, M.},
+    title = {Towards a framework for light-dosimetry studies: {Methodological} considerations},
+    journal = {Lighting Research \& Technology},
+    volume = {55},
+    number = {4-5},
+    pages = {377--399},
+    doi = {10.1177/14771535221103258},
+    year = {2023}
+}
+
+@article{lazar2024,
+    author = {Lazar, Rafael and Fazlali, Fatemeh and Dourte, Marine and Epple, Christian and Stefani, Oliver and Spitschan, Manuel and Cajochen, Christian},
+    title = {Afternoon to early evening bright light exposure reduces later melatonin production in adolescents [preprint]},
+    journal = {bioRxiv},
+    year = {2024},
+    doi = {10.1101/2024.10.02.616112},
+    url = {https://doi.org/10.1101/2024.10.02.616112}
+}
+
+@article{migueles2019,
+    title = {GGIR: A research community-driven open source {R} package for generating physical activity and sleep outcomes from multi-day raw accelerometer data},
+    author = {Migueles, Jairo H. and Rowlands, Alex V. and Huber, Florian and Sabia, Severine and van Hees, Vincent T.},
+    journal = {Journal for the Measurement of Physical Behavior},
+    volume = {2},
+    number = {3},
+    year = {2019},
+    doi = {10.1123/jmpb.2018-0063},
+    url = {https://doi.org/10.1123/jmpb.2018-0063}
+}
+
+@software{repo,
+    title = {{L}ight{L}og{R}: {P}rocess {D}ata from {W}earable {L}ight {L}oggers and {O}ptical {R}adiation {D}osimeters. Github Repository},
+    author = {{Zauner}, {Johannes} and {Hartmeyer}, Steffen L. and {Spitschan}, {Manuel}},
+    version      = {v0.4.1},
+    year = {2023},
+    url = {https://github.com/tscnlab/LightLogR}
+}
+
+@article{roguski2024,
+    author = {Roguski, A and Needham, N and MacGillivray, T and Martinovic, J and Dhillon, B and Riha, RL and Armstrong, L and Campbell, IH and Ferguson, A and Hilgen, G and Lako, M and Ritter, P and Santhi, N and von Schantz, M and Spitschan, M and Smith, DJ},
+    title = {Investigating light sensitivity in bipolar disorder ({HELIOS-BD})},
+    journal = {Wellcome Open Research},
+    volume = {9},
+    pages = {64},
+    doi = {10.12688/wellcomeopenres.20557.1},
+    pmid = {38716042},
+    pmcid = {PMC11074697},
+    month = {Feb},
+    year = {2024}
+}
+
+@article{spitschan2022,
+    author = {Spitschan, Manuel and Smolders, Karin and Vandendriessche, Benjamin and Bent, Brinnae and Bakker, Jessie P and Rodriguez-Chavez, Isaac R and Vetter, Céline},
+    title = {Verification, analytical validation and clinical validation ({V3}) of wearable dosimeters and light loggers},
+    journal = {Digital Health},
+    volume = {8},
+    pages = {20552076221144858},
+    doi = {10.1177/20552076221144858},
+    year = {2022},
+    month = {January}
+}
+
+@article{stefani2024,
+    author = {Oliver Stefani and Reto Marek and Jürg Schwarz and Sina Plate and Johannes Zauner and Björn Schrader},
+    title = {Wearable light Loggers in field conditions: {Corneal} light characteristics, user compliance and acceptance [preprint]},
+    journal = {Preprints},
+    doi = {10.20944/preprints202409.1285.v1},
+    url = {https://doi.org/10.20944/preprints202409.1285.v1},
+    publisher = {Preprints},
+    month = {September},
+    year = {2024}
+}
+
+@article{spitschan2024,
+    author = {Manuel Spitschan and Johannes Zauner and Maria {Nilsson Tengelin} and Constantinos A. Bouroussis and Patrik Caspar and Fabien Eloi},
+    title = {Illuminating the future of wearable light metrology: Overview of the MeLiDos Project},
+    journal = {Measurement},
+    volume = {235},
+    pages = {114909},
+    doi = {10.1016/j.measurement.2024.114909},
+    url = {https://www.sciencedirect.com/science/article/pii/S0263224124007942},
+    issn = {0263-2241},
+    year = {2024}
+}
+
+@misc{tutorial,
+	author = {{Zauner}, {Johannes} and {Hartmeyer}, Steffen L. and {Spitschan}, {Manuel}},
+	title = {{L}ight{L}og{R}: Tutorial: The whole game},
+	howpublished = {\url{https://tscnlab.github.io/LightLogR/articles/Day.html}},
+	year = {2023},
+	note = {[Accessed 07-10-2024]},
+}
+
+@article{wilkinson2016,
+    author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and 't Hoen, Peter A. C. and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Barend and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, A.},
+    title = {The {FAIR Guiding Principles} for scientific data management and stewardship},
+    journal = {Scientific Data},
+    volume = {3},
+    pages = {160018},
+    doi = {10.1038/sdata.2016.18},
+    url = {https://doi.org/10.1038/sdata.2016.18},
+    year = {2016}
+}
+
+@book{wickham2016,
+    author = {Hadley Wickham},
+    title = {ggplot2: Elegant Graphics for Data Analysis},
+    publisher = {Springer-Verlag New York},
+    year = {2016},
+    isbn = {978-3-319-24277-4},
+    url = {https://ggplot2.tidyverse.org}
+  }
+
+@article{zauner2023,
+    author = {Zauner, Johannes and Udovicic, Ljiljana and Spitschan, Manuel},
+    title = {Power analysis for personal light exposure measurements and interventions [preprint]},
+    journal = {Research Square},
+    doi = {10.21203/rs.3.rs-3771881/v1},
+    year = {2023}
+}
+
+@software{zenodo,
+  author       = {{Zauner}, {Johannes} and {Hartmeyer}, Steffen L. and {Spitschan}, {Manuel}},
+  title        = {tscnlab/LightLogR: v0.4.1. Archive},
+  month        = sep,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v0.4.1},
+  doi          = {10.5281/zenodo.13839724},
+  url          = {https://doi.org/10.5281/zenodo.13839724}
+}