Address reviewer feedback

Author: Max Czapanskiy

README.Rmd

@@ -17,6 +17,8 @@ Authors <- "Czapanskiy, M. F., Ponganis, P. J., Fahlbusch, J. A., and Goldbogen,
 
 # cetaceanbcg
 
+[![DOI](https://zenodo.org/badge/399999855.svg)](https://zenodo.org/badge/latestdoi/399999855)
+
 This repository contains the data and code for our paper:
 
 > `r Authors` (in prep). _`r Title`_.

README.md

@@ -3,7 +3,7 @@
 
 # cetaceanbcg
 
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/FlukeAndFeather/cetaceanbcg/main?urlpath=rstudio)
+[![DOI](https://zenodo.org/badge/399999855.svg)](https://zenodo.org/badge/latestdoi/399999855)
 
 This repository contains the data and code for our paper:
 
@@ -18,7 +18,7 @@ Following publication, please cite this compendium as:
 > Czapanskiy, M. F., Ponganis, P. J., Fahlbusch, J. A., and Goldbogen,
 > J. A. (2021). *Compendium of R code and data for “An
 > accelerometer-derived ballistocardiogram method for detecting
-> heartrates in free-ranging marine mammals”*. Accessed 27 Oct 2021.
+> heartrates in free-ranging marine mammals”*. Accessed 03 Dec 2021.
 
 ## Contents
 
@@ -37,7 +37,7 @@ The **analysis** directory contains:
     Supplementary materials including notes and other documents prepared
     and collected during the analysis.
 
-## How to run in your broswer or download and run locally
+## How to download and run locally
 
 This research compendium has been developed using the statistical
 programming language R. To work with the compendium, you will need

analysis/figures/bw-bcg-1.png

@@ -1,3 +1,14 @@
+@software{cetaceanbcgzenodo,
+  author       = {Max Czapanskiy},
+  title        = {FlukeAndFeather/cetaceanbcg: Pre-print},
+  month        = dec,
+  year         = 2021,
+  publisher    = {Zenodo},
+  version      = {v0.1.0},
+  doi          = {10.5281/zenodo.5753233},
+  url          = {https://doi.org/10.5281/zenodo.5753233}
+}
+
 @Manual{R-bookdown,
   title = {bookdown: Authoring Books and Technical Documents with R Markdown},
   author = {Yihui Xie},

analysis/figures/bw-validation-plots-1.png

@@ -505,7 +505,7 @@ @article{bickettHeartRatesHeart2019
 }
 
 @article{ponganisHeartRateElectrocardiogram1999,
-	title = {Heart {Rate} and {Electrocardiogram} {Characteristics} of a {Young} {California} {Gray} {Whale} (eschrichtius {Robustus})1},
+	title = {Heart {Rate} and {Electrocardiogram} {Characteristics} of a {Young} {California} {Gray} {Whale} (\textit{Eschrichtius robustus})},
 	volume = {15},
 	issn = {1748-7692},
 	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1748-7692.1999.tb00885.x},
@@ -571,7 +571,208 @@ @article{andreozzi2021
 	month = {11},
 	date = {2021-11-18},
 	journal = {Frontiers in Physiology},
+	pages = {725716},
 	volume = {12},
 	doi = {10.3389/fphys.2021.725716},
 	url = {http://dx.doi.org/10.3389/fphys.2021.725716}
 }
+
+@article{patterson2019,
+	title = {A comparison of techniques for classifying behavior from accelerometers for two species of seabird},
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+	year = {2019},
+	month = {02},
+	date = {2019-02-21},
+	journal = {Ecology and Evolution},
+	pages = {3030--3045},
+	volume = {9},
+	number = {6},
+	doi = {10.1002/ece3.4740},
+	url = {http://dx.doi.org/10.1002/ece3.4740},
+	langid = {en}
+}
+
+@article{divirgilio2018,
+	title = {Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management},
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+	journal = {PeerJ},
+	pages = {e4867},
+	volume = {6},
+	doi = {10.7717/peerj.4867},
+	url = {http://dx.doi.org/10.7717/peerj.4867},
+	langid = {en}
+}
+
+@article{kim2016,
+	title = {Ballistocardiogram: Mechanism and Potential for Unobtrusive Cardiovascular Health Monitoring},
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+	url = {http://dx.doi.org/10.1038/srep31297},
+	langid = {en}
+}
+
+@article{goldbogen2006,
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+	date = {2006-04-01},
+	journal = {Journal of Experimental Biology},
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+	url = {http://dx.doi.org/10.1242/jeb.02135},
+	langid = {en}
+}
+
+@article{Stahl1967b,
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+	date = {1967-03-01},
+	journal = {Journal of Applied Physiology},
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+	url = {http://dx.doi.org/10.1152/jappl.1967.22.3.453},
+	langid = {en}
+}
+
+@article{martínlópez2021,
+	title = {Overall dynamic body acceleration measures activity differently on large versus small aquatic animals},
+	author = {{Martín López}, {Lucía Martina} and {Aguilar de Soto}, {Natacha} and {Madsen}, {Peter T.} and {Johnson}, {Mark}},
+	year = {2021},
+	month = {11},
+	date = {2021-11-10},
+	journal = {Methods in Ecology and Evolution},
+	doi = {10.1111/2041-210x.13751},
+	url = {http://dx.doi.org/10.1111/2041-210X.13751},
+	langid = {en}
+}
+
+@article{samann2019,
+	title = {An efficient ECG Denoising method using Discrete Wavelet with Savitzky-Golay filter},
+	author = {{Samann}, {Fars} and {Schanze}, {Thomas}},
+	year = {2019},
+	month = {09},
+	date = {2019-09-01},
+	journal = {Current Directions in Biomedical Engineering},
+	pages = {385--387},
+	volume = {5},
+	number = {1},
+	doi = {10.1515/cdbme-2019-0097},
+	url = {http://dx.doi.org/10.1515/cdbme-2019-0097},
+	langid = {en}
+}
+
+@article{noren2012,
+	title = {The dive response redefined: underwater behavior influences cardiac variability in freely diving dolphins},
+	author = {{Noren}, {Shawn R.} and {Kendall}, {Traci} and {Cuccurullo}, {Veronica} and {Williams}, {Terrie M.}},
+	year = {2012},
+	month = {08},
+	date = {2012-08-15},
+	journal = {Journal of Experimental Biology},
+	pages = {2735--2741},
+	volume = {215},
+	number = {16},
+	doi = {10.1242/jeb.069583},
+	url = {http://dx.doi.org/10.1242/jeb.069583},
+	langid = {en}
+}
+
+@article{moukadem2018,
+	title = {Time-Frequency Domain for BCG Analysis},
+	author = {{Moukadem}, {Ali} and {Finnaoui}, {Azzeddine} and {Gassara}, {Houssem E.} and {Adolphe}, {Dominique} and {Schacher}, {Laurence} and {Dieterlen}, {Alain}},
+	year = {2018},
+	month = {08},
+	date = {2018-08},
+	journal = {2018 International Conference on Computer and Applications (ICCA)},
+	doi = {10.1109/comapp.2018.8460408},
+	url = {http://dx.doi.org/10.1109/COMAPP.2018.8460408}
+}
+
+@article{nassar2018,
+	title = {Compliant lightweight non-invasive standalone {\textquotedblleft}Marine Skin{\textquotedblright} tagging system},
+	author = {{Nassar}, {Joanna M.} and {Khan}, {Sherjeel M.} and {Velling}, {Seneca J.} and {Diaz-Gaxiola}, {Andrea} and {Shaikh}, {Sohail F.} and {Geraldi}, {Nathan R.} and {Torres Sevilla}, {Galo A.} and {Duarte}, {Carlos M.} and {Hussain}, {Muhammad M.}},
+	year = {2018},
+	month = {05},
+	date = {2018-05-03},
+	journal = {npj Flexible Electronics},
+	volume = {2},
+	number = {1},
+	doi = {10.1038/s41528-018-0025-1},
+	url = {http://dx.doi.org/10.1038/s41528-018-0025-1},
+	langid = {en}
+}
+
+@article{andrews2008,
+	title = {Satellite tracking reveals distinct movement patterns for Type B and Type C killer whales in the southern Ross Sea, Antarctica},
+	author = {{Andrews}, {Russel D.} and {Pitman}, {Robert L.} and {Ballance}, {Lisa T.}},
+	year = {2008},
+	month = {07},
+	date = {2008-07-30},
+	journal = {Polar Biology},
+	pages = {1461--1468},
+	volume = {31},
+	number = {12},
+	doi = {10.1007/s00300-008-0487-z},
+	url = {http://dx.doi.org/10.1007/s00300-008-0487-z},
+	langid = {en}
+}
+
+@article{southall2019,
+	title = {Behavioral responses of individual blue whales (Balaenoptera musculus) to mid-frequency military sonar},
+	author = {{Southall}, {Brandon L.} and {DeRuiter}, {Stacy L.} and {Friedlaender}, {Ari} and {Stimpert}, {Alison K.} and {Goldbogen}, {Jeremy A.} and {Hazen}, {Elliott} and {Casey}, {Caroline} and {Fregosi}, {Selene} and {Cade}, {David E.} and {Allen}, {Ann N.} and {Harris}, {Catriona M.} and {Schorr}, {Greg} and {Moretti}, {David} and {Guan}, {Shane} and {Calambokidis}, {John}},
+	year = {2019},
+	month = {03},
+	date = {2019-03-01},
+	journal = {Journal of Experimental Biology},
+	volume = {222},
+	number = {5},
+	doi = {10.1242/jeb.190637},
+	url = {http://dx.doi.org/10.1242/jeb.190637},
+	langid = {en}
+}
+
+@article{goldbogen2019,
+	title = {Why whales are big but not bigger: Physiological drivers and ecological limits in the age of ocean giants},
+	author = {{Goldbogen}, {Jeremy A.} and {Cade}, {D. E.} and {Wisniewska}, {D. M.} and {Potvin}, {J.} and {Segre}, {P. S.} and {Savoca}, {M. S.} and {Hazen}, {E. L.} and {Czapanskiy}, {M. F.} and {Kahane-Rapport}, {S. R.} and {DeRuiter}, {S. L.} and {Gero}, {S.} and {Tønnesen}, {P.} and {Gough}, {W. T.} and {Hanson}, {M. B.} and {Holt}, {M. M.} and {Jensen}, {F. H.} and {Simon}, {M.} and {Stimpert}, {A. K.} and {Arranz}, {P.} and {Johnston}, {D. W.} and {Nowacek}, {D. P.} and {Parks}, {S. E.} and {Visser}, {F.} and {Friedlaender}, {A. S.} and {Tyack}, {P. L.} and {Madsen}, {P. T.} and {Pyenson}, {N. D.}},
+	year = {2019},
+	month = {12},
+	date = {2019-12-13},
+	journal = {Science},
+	pages = {1367--1372},
+	volume = {366},
+	number = {6471},
+	doi = {10.1126/science.aax9044},
+	url = {https://science.sciencemag.org/content/366/6471/1367},
+	note = {PMID: 31831666},
+	langid = {en}
+}
+
+@article{savoca2021,
+	title = {Baleen whale prey consumption based on high-resolution foraging measurements},
+	author = {{Savoca}, {Matthew S.} and {Czapanskiy}, {Max F.} and {Kahane-Rapport}, {Shirel R.} and {Gough}, {William T.} and {Fahlbusch}, {James A.} and {Bierlich}, {K. C.} and {Segre}, {Paolo S.} and {Di Clemente}, {Jacopo} and {Penry}, {Gwenith S.} and {Wiley}, {David N.} and {Calambokidis}, {John} and {Nowacek}, {Douglas P.} and {Johnston}, {David W.} and {Pyenson}, {Nicholas D.} and {Friedlaender}, {Ari S.} and {Hazen}, {Elliott L.} and {Goldbogen}, {Jeremy A.}},
+	year = {2021},
+	month = {11},
+	date = {2021-11-03},
+	journal = {Nature},
+	pages = {85--90},
+	volume = {599},
+	number = {7883},
+	doi = {10.1038/s41586-021-03991-5},
+	url = {http://dx.doi.org/10.1038/s41586-021-03991-5},
+	langid = {en}
+}