correcting references in paper

paper/paper.Rmd

@@ -8,7 +8,7 @@ tags:
   - tree ring
   - archaeology
 authors:
-  - name: Ronald M. Visser 
+  - name: Ronald M. Visser
     orcidlink: 0000-0001-6966-1729
     affiliation: 1
 affiliations:
@@ -29,11 +29,11 @@ The R-package dendroNetwork aims to make network analyses of dendrochronological
 
 # Introduction
 
-Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparisons are often visualised as tabular data. However, to analyse the complex system of relations between tree-ring curves other methods are necessary. The author has developed a method to analyse patterns of similarity between tree-ring series using network analysis [@visser2021; @visser2022]. The analyses of these papers was mostly based on scripts that are shared with the papers [@visservorst, @visser]. For others to apply the developed method with these scripts is possible, but cumbersome and various things need to be changed. In addition, to try the network approach on dendrochronological data for the first time can be overwhelming an seemingly difficult. To make this more easy and accessible a new package for R has been designed to help users to apply this method to their data. The package dendroNetwork enables researchers to create tables with the similarity using various measures and visualize these using R [@rcoreteam2022] and Cytoscape [@otasek2019; @shannon2003a]. Cytoscape is an open source and platform independent tool for network analysis and visualization. The software provides easy visual access to complex networks and the attributes of both nodes and edges in a network. The dendroNetwork package has been reviewed on ROpenSci (<https://github.com/ropensci/dendroNetwork> and <https://docs.ropensci.org/dendroNetwork/>).
+Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparisons are often visualised as tabular data. However, to analyse the complex system of relations between tree-ring curves other methods are necessary. The author has developed a method to analyse patterns of similarity between tree-ring series using network analysis [@visser2021; @visser2022]. The analyses of these papers was mostly based on scripts that are shared with the papers [@visservorst, @visser]. For others to apply the developed method with these scripts is possible, but cumbersome and various things need to be changed. In addition, to try the network approach on dendrochronological data for the first time can be overwhelming an seemingly difficult. To make this more easy and accessible a new package for R has been designed to help users to apply this method to their data. The package dendroNetwork [@visser2024] enables researchers to create tables with the similarity using various measures and visualize these using R [@rcoreteam2022] and Cytoscape [@otasek2019; @shannon2003a]. Cytoscape is an open source and platform independent tool for network analysis and visualization. The software provides easy visual access to complex networks and the attributes of both nodes and edges in a network. The dendroNetwork package has been reviewed on ROpenSci (<https://github.com/ropensci/dendroNetwork> and <https://docs.ropensci.org/dendroNetwork/>).
 
 # Statement of need
 
-There are several packages available in R for dendrochronological research [@guiterman2020; @jevsenak2018; @campelo2012; @bunn2008; @shi2019; @vandermaaten-theunissen2015; @reynolds2021; @altman2014; @malevich2018; @rademacher; @campelo2019; @haneca2023; @alday2018]. An overview with links to these packages can be found online (<https://ronaldvisser.github.io/Dendro_R/>). Some packages are specifically creates to obtain measurements [@campelo2019; @shi2019], while others are written for crossdating [@reynolds2021]. There are also various for analysing tree-ring data [@alday2018; @alday2018; @altman2014; @bunn2008; @campelo2012; @zang2015; @guiterman2020]. These R-packages in dendrochronology all fill different needs, but the nice thing is that these are all interconnected in some way in depending on each other, or that they build further into different avenues. Apart from depending on dendrochronological packages, various packages from the Tidyverse [@wickham2019] are often also needed. The various relations can easily be visualised using a network, with the edges based on the dependency of two packages on each other, and and arrow indicating the direction of the dependency. Some R-package for dendrochronology or tree-ring studies have no relation with others, but fill specific needs [@peters2018; @lara2018; @campelo2016; @aryal2020]. These are left out of the network (see Figure \@ref(fig:packages-network)).
+There are several packages available in R for dendrochronological research [@guiterman2020; @jevsenak2018; @campelo2012; @bunn2008; @shi2019; @vandermaaten-theunissen2015; @reynolds2021; @altman2014; @malevich2018; @rademacher; @campelo2019; @haneca2024; @alday2018]. An overview with links to these packages can be found online (<https://ronaldvisser.github.io/Dendro_R/>). Some packages are specifically creates to obtain measurements [@campelo2019; @shi2019], while others are written for crossdating [@reynolds2021]. There are also various for analysing tree-ring data [@alday2018; @alday2018; @altman2014; @bunn2008; @campelo2012; @zang2015; @guiterman2020]. These R-packages in dendrochronology all fill different needs, but the nice thing is that these are all interconnected in some way in depending on each other, or that they build further into different avenues. Apart from depending on dendrochronological packages, various packages from the Tidyverse [@wickham2019] are often also needed. The various relations can easily be visualised using a network, with the edges based on the dependency of two packages on each other, and and arrow indicating the direction of the dependency. Some R-package for dendrochronology or tree-ring studies have no relation with others, but fill specific needs [@peters2018; @lara2018; @campelo2016; @aryal2020]. These are left out of the network (see Figure \@ref(fig:packages-network)).
 
 ```{r, packages-network, out.width="50%", fig.cap = "The interdependent relations between existing R-packages related to dendrochronology", echo=FALSE}
 g_dendro_packages <- igraph::graph( c("dplR", "dfoliatR", "tidyverse", "dfoliatR",

paper/paper.bib

@@ -192,13 +192,15 @@ @article{csardi2006
 
 @misc{visservorst,
 	title = {Analyses, data and figures related to: {"}Connecting ships: using dendrochronological network analysis to determine the wood provenance of Roman-period river barges found in the Lower Rhine region and to visualise patterns of wood use{"}},
-	author = {Visser, Ronald and Vorst, Yardeni},
+	author = {Visser, Ronald M. and Vorst, Yardeni},
+	year = {2022},
 	doi = {10.5281/zenodo.7243539}
 }
 
 @misc{visser,
 	title = {Dendrochronological Provenance Patterns. Code and Data of Network Analysis of Tree-Ring Material},
 	author = {Visser, Ronald M.},
+	year = {2022},
 	doi = {10.5281/zenodo.10200361}
 }
 
@@ -322,12 +324,12 @@ @article{alday2018
 	url = {http://www.sciencedirect.com/science/article/pii/S1125786517301212}
 }
 
-@book{haneca2023,
+@book{haneca2024,
 	title = {fellingdateR: an R package to facilitate the organisation, analysis and interpretation of tree-ring data from wooden heritage objects and structures},
 	author = {Haneca, Kristof},
-	year = {2023},
-	date = {2023},
-	url = {https://github.com/hanecakr/fellingDateR}
+	year = {2024},
+	date = {2024},
+	url = {https://github.com/ropensci/fellingdater}
 }
 
 @article{malevich2018,
@@ -412,3 +414,15 @@ @article{aryal2020
 	doi = {10.1016/j.dendro.2020.125772},
 	url = {https://www.sciencedirect.com/science/article/pii/S1125786520301119}
 }
+
+@book{visser2024,
+	title = {dendroNetwork: a R-package to create dendrochronological networks},
+	author = {Visser, Ronald M.},
+	year = {2024},
+	month = {04},
+	date = {2024-04-26},
+	publisher = {Zenodo},
+	doi = {10.5281/zenodo.10636310},
+	url = {https://zenodo.org/doi/10.5281/zenodo.10636310},
+	note = {DOI: 10.5281/zenodo.10636310}
+}

paper/paper.log

@@ -1,4 +1,4 @@
-This is XeTeX, Version 3.141592653-2.6-0.999996 (TeX Live 2024) (preloaded format=xelatex 2024.4.26)  27 APR 2024 12:25
+This is XeTeX, Version 3.141592653-2.6-0.999996 (TeX Live 2024) (preloaded format=xelatex 2024.4.26)  30 APR 2024 09:35
 entering extended mode
  restricted \write18 enabled.
  %&-line parsing enabled.

paper/paper.md

@@ -8,14 +8,14 @@ tags:
   - tree ring
   - archaeology
 authors:
-  - name: Ronald M. Visser 
+  - name: Ronald M. Visser
     orcidlink: 0000-0001-6966-1729
     affiliation: 1
 affiliations:
   - name: Saxion University of Applied Sciences, Deventer
     index: 1
 citation_author: Visser
-date: "27 April 2024"
+date: "30 April 2024"
 year: 2024
 bibliography: paper.bib
 output: rticles::joss_article
@@ -29,11 +29,11 @@ The R-package dendroNetwork aims to make network analyses of dendrochronological
 
 # Introduction
 
-Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparisons are often visualised as tabular data. However, to analyse the complex system of relations between tree-ring curves other methods are necessary. The author has developed a method to analyse patterns of similarity between tree-ring series using network analysis [@visser2021; @visser2022]. The analyses of these papers was mostly based on scripts that are shared with the papers [@visservorst, @visser]. For others to apply the developed method with these scripts is possible, but cumbersome and various things need to be changed. In addition, to try the network approach on dendrochronological data for the first time can be overwhelming an seemingly difficult. To make this more easy and accessible a new package for R has been designed to help users to apply this method to their data. The package dendroNetwork enables researchers to create tables with the similarity using various measures and visualize these using R [@rcoreteam2022] and Cytoscape [@otasek2019; @shannon2003a]. Cytoscape is an open source and platform independent tool for network analysis and visualization. The software provides easy visual access to complex networks and the attributes of both nodes and edges in a network. The dendroNetwork package has been reviewed on ROpenSci (<https://github.com/ropensci/dendroNetwork> and <https://docs.ropensci.org/dendroNetwork/>).
+Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparisons are often visualised as tabular data. However, to analyse the complex system of relations between tree-ring curves other methods are necessary. The author has developed a method to analyse patterns of similarity between tree-ring series using network analysis [@visser2021; @visser2022]. The analyses of these papers was mostly based on scripts that are shared with the papers [@visservorst, @visser]. For others to apply the developed method with these scripts is possible, but cumbersome and various things need to be changed. In addition, to try the network approach on dendrochronological data for the first time can be overwhelming an seemingly difficult. To make this more easy and accessible a new package for R has been designed to help users to apply this method to their data. The package dendroNetwork [@visser2024] enables researchers to create tables with the similarity using various measures and visualize these using R [@rcoreteam2022] and Cytoscape [@otasek2019; @shannon2003a]. Cytoscape is an open source and platform independent tool for network analysis and visualization. The software provides easy visual access to complex networks and the attributes of both nodes and edges in a network. The dendroNetwork package has been reviewed on ROpenSci (<https://github.com/ropensci/dendroNetwork> and <https://docs.ropensci.org/dendroNetwork/>).
 
 # Statement of need
 
-There are several packages available in R for dendrochronological research [@guiterman2020; @jevsenak2018; @campelo2012; @bunn2008; @shi2019; @vandermaaten-theunissen2015; @reynolds2021; @altman2014; @malevich2018; @rademacher; @campelo2019; @haneca2023; @alday2018]. An overview with links to these packages can be found online (<https://ronaldvisser.github.io/Dendro_R/>). Some packages are specifically creates to obtain measurements [@campelo2019; @shi2019], while others are written for crossdating [@reynolds2021]. There are also various for analysing tree-ring data [@alday2018; @alday2018; @altman2014; @bunn2008; @campelo2012; @zang2015; @guiterman2020]. These R-packages in dendrochronology all fill different needs, but the nice thing is that these are all interconnected in some way in depending on each other, or that they build further into different avenues. Apart from depending on dendrochronological packages, various packages from the Tidyverse [@wickham2019] are often also needed. The various relations can easily be visualised using a network, with the edges based on the dependency of two packages on each other, and and arrow indicating the direction of the dependency. Some R-package for dendrochronology or tree-ring studies have no relation with others, but fill specific needs [@peters2018; @lara2018; @campelo2016; @aryal2020]. These are left out of the network (see Figure \@ref(fig:packages-network)).
+There are several packages available in R for dendrochronological research [@guiterman2020; @jevsenak2018; @campelo2012; @bunn2008; @shi2019; @vandermaaten-theunissen2015; @reynolds2021; @altman2014; @malevich2018; @rademacher; @campelo2019; @haneca2024; @alday2018]. An overview with links to these packages can be found online (<https://ronaldvisser.github.io/Dendro_R/>). Some packages are specifically creates to obtain measurements [@campelo2019; @shi2019], while others are written for crossdating [@reynolds2021]. There are also various for analysing tree-ring data [@alday2018; @alday2018; @altman2014; @bunn2008; @campelo2012; @zang2015; @guiterman2020]. These R-packages in dendrochronology all fill different needs, but the nice thing is that these are all interconnected in some way in depending on each other, or that they build further into different avenues. Apart from depending on dendrochronological packages, various packages from the Tidyverse [@wickham2019] are often also needed. The various relations can easily be visualised using a network, with the edges based on the dependency of two packages on each other, and and arrow indicating the direction of the dependency. Some R-package for dendrochronology or tree-ring studies have no relation with others, but fill specific needs [@peters2018; @lara2018; @campelo2016; @aryal2020]. These are left out of the network (see Figure \@ref(fig:packages-network)).
 
 \begin{figure}
 \includegraphics[width=0.5\linewidth]{paper_files/figure-latex/packages-network-1} \caption{The interdependent relations between existing R-packages related to dendrochronology}\label{fig:packages-network}