Paper updates with more references and clarification

paper/paper.bib

@@ -27,7 +27,7 @@ @book{wickham:2016
 }
 
 @article{rougier:2014,
-  author = {Rougier, Nicolas P. and Droettboom, Michael and Bourne, Philip E.},
+  author = {Rougier, Nicolas P. AND Droettboom, Michael AND Bourne, Philip E.},
   doi = {10.1371/journal.pcbi.1003833},
   issn = {1553-7358},
   journal = {PLoS Computational Biology},
@@ -39,3 +39,30 @@ @article{rougier:2014
   volume = {10},
   year = {2014}
 }
+
+@article{nunez:2018,
+    doi = {10.1371/journal.pone.0199239},
+    author = {Nuñez, Jamie R. AND Anderton, Christopher R. AND Renslow, Ryan S.},
+    journal = {PLOS ONE},
+    publisher = {Public Library of Science},
+    title = {Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data},
+    year = {2018},
+    month = {08},
+    volume = {13},
+    url = {https://doi.org/10.1371/journal.pone.0199239},
+    pages = {1-14},
+    number = {7},
+}
+
+@article{crameri:2020,
+    doi = {10.1038/s41467-020-19160-7},
+    author = {Crameri, Fabio AND Shephard, Grace E. AND Heron, Philip J.},
+    journal = {Nature Communications},
+    publisher = {Springer Nature},
+    title = {The misuse of colour in science communication},
+    year = {2020},
+    month = {10},
+    volume = {11},
+    url = {https://www.nature.com/articles/s41467-020-19160-7},
+    pages = {5444-5454},
+}

paper/paper.md

@@ -1,19 +1,20 @@
 ---
 title: 'PlotFTIR: Plotting FTIR Spectra'
 tags:
-  - R
-  - spectroscopy
-  - visualization
-  - chemometrics
+- R
+- spectroscopy
+- visualization
+- chemometrics
+date: "13 December 2024"
+output: pdf_document
 authors:
-  - name: Philip Bulsink
-    orcid: 0000-0001-9668-2429
-    affiliation: 1
-affiliations:
- - name: CanmetENERGY-Ottawa, Natural Resources Canada
-   index: 1
-date: 22 October 2024
+- name: Philip Bulsink
+  orcid: "0000-0001-9668-2429"
+  affiliation: 1
 bibliography: paper.bib
+affiliations:
+- name: "CanmetENERGY-Ottawa, Natural Resources Canada"
+  index: 1
 ---
 
 # Summary
@@ -26,11 +27,11 @@ absorbance values and can be used to confirm the identity of a chemical or the c
 
 These infra-red absorbance measurements are commonly performed on Fourier Transform Infra-red (FTIR) instruments. Scientists
 and researchers may compare different FTIR spectra to observe changes in concentration of components, or changes in the
-bond properties in a sample after a manipulation in the laboratory. These comparisons may be simple graphical comparisons, 
+bond properties in a sample after a manipulation in the laboratory. These comparisons may be simple graphical comparisons or they 
 or use advanced statistical tools such as PCA/PCR or chemometrics to deduce properties. Regardless of the analysis, 
 scientists and researchers often need to publish FTIR spectra in journal articles. 
 
-This package provides a convenient and reproducible workflow option for the production of graphics with minor spectra
+This package provides a convenient and reproducible workflow option for the production of graphics, and includes minor spectra
 manipulation capabilities.
 
 # Statement of need
@@ -39,8 +40,8 @@ manipulation capabilities.
 with high-quality defaults (\autoref{fig:example}). Scientists and researchers often rely on manual processes in software 
 (such as Excel) to produce graphics for journals, but these can be cumbersome and slow, requiring manual changes as new data 
 is produced, or difficult changes if the researcher needs to perform even simple data manipulation (such as shifting spectra 
-or averaging results). Key components of producing high-quality figures are outlined by Rougier et. al. [@rougier:2014] and 
-the core principle of `PlotFTIR` is to follow these 'simple rules'.
+or averaging results). Key components of producing high-quality figures are outlined by @rougier:2014 and 
+the core principle of `PlotFTIR` is to enable scientists and researchers to follow these 'simple rules'.
 
 ![Example FTIR spectra produced by `PlotFTIR`.\label{fig:example}](./paper-biodiesel.png)
 
@@ -57,22 +58,22 @@ packages. This permits complex baseline, smoothing, or derivative calculations i
 clustering, or ANOVA in `ChemoSpec`, and finishing with pretty plotting in `PlotFTIR`, all in one workflow. 
 
 `PlotFTIR` supports annotation of graphics with markers and labels, simple title and legend changes, sample renaming
-functions, and output options. It also provides logical default graphical parameters, including titles, legends, 
+functions, and output options. It also provides domain-specific default graphical parameters, including titles, legends, 
 axis labels, color palettes, and the inversion of the x-axis typical of IR spectral images. It does this in contrast to 
 the other `R` packages for FTIR  which focus on spectra statistics or processing, but ignore the graphical requirements 
 of publishing journal articles or reports (i.e. producing plots with normal x-axis orientation, default ggplot2 colour 
-palettes and labels, no support for annotation beyond ggplot functions, etc.) [@teickner:2022; @hanson:2024]. 
+palettes and labels, no support for annotation without directly using ggplot functions, etc.) [@teickner:2022; @hanson:2024]. 
 
 While `PlotFTIR` produces graphics using `ggplot2` [@wickham:2016], it enables novice users to produce graphics easily 
 without preventing advanced users from performing customization. Users need not know `ggplot2` functions to produce 
 `PlotFTIR` graphics, instead, the graphical functions in `PlotFTIR` are designed to be used in a traditional step-wise 
 or piped fashion where multiple graphical manipulations can be performed sequentially. However, should users more 
 comfortable with `R` and `ggplot2` feel the need, the entire plot can be modified to their purposes with `ggplot2` 
-manipulations.
-
-The documentation for `PlotFTIR` is available in English and French (including having default French labels and titles
-available for plotting by setting `lang = 'fr'` in the initial arguments for the plot). 
+manipulations. `PlotFTIR` uses, by default, colourblind-friendly palettes following best practices at outline elsewhere 
+[@nunez:2018; @crameri:2020]. 
 
+The documentation for `PlotFTIR` is available in English and French (including having default French language labels 
+and titles available for plotting by setting `lang = 'fr'` in the initial arguments for the plot or as a system option). 
 
 # Acknowledgements