added descriptions of Cytoscape in the readme and vignettes

Author: RonaldVisser

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dendroNetwork
 Type: Package
 Title: Create networks of dendrochronological series using pairwise similarity
-Version: 0.5.2
+Version: 0.5.3
 Authors@R: 
     c(person(given = "Ronald", 
             family = "Visser", 

NEWS.md

@@ -12,6 +12,8 @@
 
 ### Documentation fixes
 
+-   added descriptions of Cytoscape in the readme and vignettes
+
 ### Continous integration
 
 ## dendroNetwork 0.5.2

README.Rmd

@@ -35,7 +35,7 @@ if (!require("BiocManager", quietly = TRUE))
 BiocManager::install("RCy3")
 ```
 
-The functionaliy of RCy3 depends on the installation of Cytoscape. It is therefore recommended to install Cyscape as well. Please follow the download and installation instructions for your operating system: <https://cytoscape.org/>.
+The functionaliy of RCy3 depends on the installation of Cytoscape. Cytoscape is needed for visualising the networks. This open source software is platform independent and provides easy visual access to complex networks and the attributes of both nodes and edges in a network (see the [Cytoscape-website](https://cytoscape.org/what_is_cytoscape.html) for more information). It is therefore recommended to install Cyscape as well. Please follow the download and installation instructions for your operating system: <https://cytoscape.org/>.
 
 You can install the development version of dendroNetwork from [GitHub](https://github.com/RonaldVisser/DendroNetwork) with:
 

README.md

@@ -43,10 +43,15 @@ if (!require("BiocManager", quietly = TRUE))
 BiocManager::install("RCy3")
 ```
 
-The functionaliy of RCy3 depends on the installation of Cytoscape. It is
-therefore recommended to install Cyscape as well. Please follow the
-download and installation instructions for your operating system:
-<https://cytoscape.org/>.
+The functionaliy of RCy3 depends on the installation of Cytoscape.
+Cytoscape is needed for visualising the networks. This open source
+software is platform independent and provides easy visual access to
+complex networks and the attributes of both nodes and edges in a network
+(see the
+[Cytoscape-website](https://cytoscape.org/what_is_cytoscape.html) for
+more information). It is therefore recommended to install Cyscape as
+well. Please follow the download and installation instructions for your
+operating system: <https://cytoscape.org/>.
 
 You can install the development version of dendroNetwork from
 [GitHub](https://github.com/RonaldVisser/DendroNetwork) with:

man/figures/README-network_hollstein_1980-1.png

@@ -35,7 +35,7 @@ text-align: justify}
 ```
 # Introduction
 
-Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparions 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 [@visser; @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].
+Dendrochronological analyses are often based on the comparison of tree-ring series with other tree-ring series. These comparions 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 [@visser; @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. The software provides easy visual access to complex networks and the attributes of both nodes and edges in a network.
 
 # Statement of need
 

man/figures/README-network_hollstein_1980-2.png

@@ -20,7 +20,7 @@ library(dendroNetwork)
 
 # Required Software
 
-dendroNetwork uses RCy3 (<https://www.bioconductor.org/packages/release/bioc/html/RCy3.html>) to connect with Cytoscape and visualize networks. You will need to install and launch Cytoscape:
+dendroNetwork uses RCy3 (<https://www.bioconductor.org/packages/release/bioc/html/RCy3.html>) to connect with Cytoscape and visualize networks. Cytoscape is open source software and platform independent and provides easy visual access to complex networks, including the attributes of both nodes and edges in a network (see the [Cytoscape-website](https://cytoscape.org/what_is_cytoscape.html) for more information). You will need to install and launch Cytoscape:
 
 -   Download the latest Cytoscape from <http://www.cytoscape.org/download.php>
 

paper/paper.Rmd

@@ -15,7 +15,7 @@ The package is written for dendrochronologists and have a general knowledge on t
 
 ## Usage {#usage}
 
-The package aims to make the creation of dendrochronological (provenance) networks as easy as possible. To be able to make use of all options, it is assumed that Cytoscape [@shannon2003] is installed (<https://cytoscape.org/>). Some data is included in this package, namely the Roman data published by Hollstein [@hollstein1980].
+The package aims to make the creation of dendrochronological (provenance) networks as easy as possible. To be able to make use of all options, it is assumed that Cytoscape [@shannon2003] is installed (<https://cytoscape.org/>). Cytoscape is open source software and platform independent and provides easy visual access to complex networks, including the attributes of both nodes and edges in a network (see the [Cytoscape-website](https://cytoscape.org/what_is_cytoscape.html) for more information). Some data is included in this package, namely the Roman data published by Hollstein [@hollstein1980].
 
 The first steps are visualized in the flowchart below, including community detection using either (or both) the Girvan-Newman algorithm [@girvan2002] and Clique Percolation Method [@palla2005] for all clique sizes. Both methods are explained very well in the papers, and on wikipedia for both [CPM](https://en.wikipedia.org/wiki/Clique_percolation_method) and the [Girvan-Newman algorithm](https://en.wikipedia.org/wiki/Girvan%E2%80%93Newman_algorithm).