Update references

Fix for #14 .

Author: samhforbes

README.Rmd

@@ -81,17 +81,17 @@ vignette('PupillometryR')
 ## Getting help
 
 Please use the issues tab (https://github.com/samhforbes/PupillometryR/issues) to file any bugs or suggestions.
-For general pupillometry information, I recommend [Sylvain's website](https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=), for reading about using GAMs in pupillometry [this paper by van Rij et al. is excellent](https://journals.sagepub.com/doi/10.1177/2331216519832483), for general GAMs knowledge I recommend [this tutorial by Michael Clark](https://m-clark.github.io/generalized-additive-models/case_for_gam.html) as well as the mgcv documentation, and for general FDA information [this website is helpful](https://www.psych.mcgill.ca/misc/fda/resources.html), along with the Ramsey and Silverman book. Additionally, check out the raincloud plots paper by Allen et al., which is used for some of the in-built plotting in this package [here](http://doi.org/10.1044/1092-4388(2010/09-0205)).
+For general pupillometry information, I recommend [Sylvain's website](https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=), [as well as Jackson and Sirois (2009)](http://doi.org/10.1111/j.1467-7687.2008.00805.x). For reading about using GAMs in pupillometry [this paper by van Rij et al. is excellent](https://journals.sagepub.com/doi/10.1177/2331216519832483), for general GAMs knowledge I recommend [this tutorial by Michael Clark](https://m-clark.github.io/generalized-additive-models/case_for_gam.html) as well as the mgcv documentation, and for general FDA information [this website is helpful](http://www.psych.mcgill.ca/misc/fda/resources.html), along with the Ramsay and Silverman book (1997). Additionally, check out the [raincloud plots paper by Allen et al.](https://wellcomeopenresearch.org/articles/4-63#:~:text=In%20essence%2C%20raincloud%20plots%20combine,error%2C%20such%20as%20a%20boxplot.), which is used for some of the in-built plotting in this package.
 
 ## Acknowledgements
 
-This package has had suggestions, encouragement, and help from a number of people, but I wish to especially highlight Sylvain Sirois and Mihaela Duta, whose input has been instrumental. I'd also like to thank Jacolien van Rij for her input with the GAMMs modelling portion of this tutorial.
+This package has had suggestions, encouragement, and help from a number of people, but I wish to especially highlight Sylvain Sirois and Mihaela Duta, whose input has been instrumental. I'd also like to thank Jacolien van Rij for her input with the GAMs modelling portion of this tutorial.
 
 ## References
 
 [1] Jackson, I., & Sirois, S. (2009). Infant cognition: Going full factorial with pupil dilation. *Developmental Science*, 12(4), 670-679. http://doi.org/10.1111/j.1467-7687.2008.00805.x
 
-[2] Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R., & Kievit, R. (2018). Raincloud plots: a multi-platform tool for robust data visualization. *Wellcome Open Research*, 4, 63.
+[2] Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R., & Kievit, R. (2018). Raincloud plots: a multi-platform tool for robust data visualization. *Wellcome Open Research*, 4, 1-41.
 doi:10.12688/wellcomeopenres.15191.1
 
 [3] Ramsay, J.O., & Silverman, B.W. (1997). *Functional data analysis*. New York: Springer-Verlag.

README.md

@@ -98,25 +98,25 @@ Please use the issues tab
 or suggestions. For general pupillometry information, I recommend
 [Sylvain’s
 website](https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=https://oraprdnt.uqtr.uquebec.ca/pls/public/gscw031?owa_no_site=314&owa_no_fiche=3&owa_bottin=),
-for reading about using GAMs in pupillometry [this paper by van Rij et
-al. is
+[as well as Jackson and Sirois
+(2009)](http://doi.org/10.1111/j.1467-7687.2008.00805.x). For reading
+about using GAMs in pupillometry [this paper by van Rij et al. is
 excellent](https://journals.sagepub.com/doi/10.1177/2331216519832483),
 for general GAMs knowledge I recommend [this tutorial by Michael
 Clark](https://m-clark.github.io/generalized-additive-models/case_for_gam.html)
 as well as the mgcv documentation, and for general FDA information [this
-website is
-helpful](https://www.psych.mcgill.ca/misc/fda/resources.html), along
-with the Ramsey and Silverman book. Additionally, check out the
-raincloud plots paper by Allen et al., which is used for some of the
-in-built plotting in this package
-[here](http://doi.org/10.1044/1092-4388\(2010/09-0205\)).
+website is helpful](http://www.psych.mcgill.ca/misc/fda/resources.html),
+along with the Ramsay and Silverman book (1997). Additionally, check out
+the [raincloud plots paper by Allen et
+al.](https://wellcomeopenresearch.org/articles/4-63#:~:text=In%20essence%2C%20raincloud%20plots%20combine,error%2C%20such%20as%20a%20boxplot.),
+which is used for some of the in-built plotting in this package.
 
 ## Acknowledgements
 
 This package has had suggestions, encouragement, and help from a number
 of people, but I wish to especially highlight Sylvain Sirois and Mihaela
 Duta, whose input has been instrumental. I’d also like to thank Jacolien
-van Rij for her input with the GAMMs modelling portion of this tutorial.
+van Rij for her input with the GAMs modelling portion of this tutorial.
 
 ## References
 
@@ -126,7 +126,7 @@ factorial with pupil dilation. *Developmental Science*, 12(4), 670-679.
 
 \[2\] Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R., & Kievit,
 R. (2018). Raincloud plots: a multi-platform tool for robust data
-visualization. *Wellcome Open Research*, 4, 63.
+visualization. *Wellcome Open Research*, 4, 1-41.
 <doi:10.12688/wellcomeopenres.15191.1>
 
 \[3\] Ramsay, J.O., & Silverman, B.W. (1997). *Functional data

paper/paper.bib

@@ -37,6 +37,14 @@ @article{Mathot2018
     keywords = {Baseline correction, Pupil size, Pupillometry, Research methods}
 }
 
+@misc{Ramsay2020,
+author = {Ramsay, J. O. and {Graves S.} and Hooker, G.},
+title = {{fda: Functional Data Analysis}},
+year = {2020}
+url = {https://CRAN.R-project.org/package=fda }
+}
+
+
 @article{Hershman2019,
     title = {{CHAP: Open-source software for processing and analyzing pupillometry data}},
     year = {2019},

paper/paper.md

@@ -34,7 +34,7 @@ Thus PupillometryR aims to assist experimenters by providing a clear pipeline wh
 
 ![An example of a raincloud plot of pupil data in PupillometryR.](Raincloud.pdf)
 
-`PupillometryR` extends a suggested pipeline for implementation of pupillometric studies [@Jackson2009], making heavy use of the `signal` package [@signal2014] for pre-processing of the pupil data. The in-built plotting functions, designed for ease of use, rely on `ggplot2` [@Wickham2016] for the data visualisation, and include raincloud plots [@Allen2019] as an in-built data visualisation option. For analysis several options are given, including the use of Generalised Additive Models which uses the `mgcv` package [@Wood2017], and Functional Data Analysis, which uses functions from the `fda` package [@Ramsay1997].
+`PupillometryR` extends a suggested pipeline for implementation of pupillometric studies [@Jackson2009], making heavy use of the `signal` package [@signal2014] for pre-processing of the pupil data. The in-built plotting functions, designed for ease of use, rely on `ggplot2` [@Wickham2016] for the data visualisation, and include raincloud plots [@Allen2019] as an in-built data visualisation option. For analysis several options are given, including the use of Generalised Additive Models which uses the `mgcv` package [@Wood2017], and Functional Data Analysis, which uses functions from the `fda` package [@Ramsay2020].
 
 ![An example of a functional t-test in PupillometryR.](FDA.pdf)