v1.0.0

.github/CONTRIBUTING.md

@@ -1,51 +1,39 @@
 # Contributing
 
-Contributions to `roctopus`, 
+Contributions to `manynet`, 
 whether in the form of issue identification, bug fixes, new code or documentation 
 are encouraged and welcome.
 
 ## Git and Bitbucket
 
-The `gnevar` project is maintained using the git version control system.
+`stocnet` projects are maintained using the git version control system.
 A plain-English introduction to git can be found [here](https://blog.red-badger.com/2016/11/29/gitgithub-in-plain-english).
 I recommend you read this before continuing. 
+A more recent motivation can be found [here](https://www.r-bloggers.com/2024/04/git-gud-version-control-best-practices/).
 It will explain the basics of git version control, committing and repos, pulling and pushing,
 branching and merging.
 
-However, one important difference from that link is that 
-instead of Github or Gitlab for hosting the remote (online) git repo,
-we will be using Bitbucket (which is actually very similar to Github and Gitlab in most respects).
 Using git from the command line on your lap- or desktop can be intimidating,
-but helpfully Atlassian (the company behind Bitbucket) have released a software interface
-for Mac and Windows called [Sourcetree](https://www.sourcetreeapp.com)
-that allows mostly visual management of commits, diffs, branches, etc.
-There are various other git software packages available, but this one is fairly full featured.
+but I recommend [Fork](https://git-fork.com) software for Mac and Windows.
+This allows mostly visual management of commits, diffs, branches, etc.
+There are various other git software packages available, but this one is fairly fully featured.
 
-The Bitbucket page allows to access the issues assigned to you and check the commits.
-You can also access the documents in the repository, altough this won't be necessary after you have
-cloned it on your computer via Sourcetree (if you open the file via Bitbucket, Sourcetree will
-not be able to identify the changes you made).
+The Github page allows to access the issues assigned to you and check the commits.
+You can also access the documents in the repository, 
+although this won't be necessary after you have cloned it on your computer via Fork.
 
-## Sourcetree
+## Style
+
+In terms of style, we are aiming for pleasant predictability in terms of user experience.
+To that end, we have a regular syntax that users can rely on producing expected effects.
+
+## Fork
 
 ### Cloning
-Once you have downloaded Sourcetree, the first thing you have to do is to 
+Once you have downloaded Fork, the first thing you have to do is to 
 clone the remote repository on your computer. 
-This is easily done by using point and click from Sourcetree
-(file, new, clone from URL) and copying the link [clone](https://[email protected]/jhollway/gnevar.git).
 Before cloning, you will be able to choose on which `branch` you want to work: 
-develop or master. 
-Working on master means you will not be altering the main workflow, whereas 
-creating a develop branch will separate your work from modifications 
-done on the master branch and be merged later on to the master branch.
-Working on master is fine as long as there are not a lot of contributors. 
-Once more people are working, it is suitable to create local branches for each 
-contributor and merge them to master when controlled by the coordinator 
-(via the `Pull request` that will allow other contributor to check your work 
-and validate it for merging)
-Note that you can still create a develop branch afterwards, 
-but make sure to pull all modifications before doing so to avoid conflicts. 
-You can find more information on creating a new branch on [branch](https://confluence.atlassian.com/sourcetreekb/branch-management-785325799.html). 
+develop or main. 
 
 ### Pull 
 This command allows you to `pull` changes from the remote repository to your local repository on Sourcetree.
@@ -54,26 +42,23 @@ When pulling, make sure you choose master or develop,
 depending on the branch you decided to work with. 
 Once you pulled, you have now all the new commits and files and 
 you can start working on your assigned tasks.
-Note that you can access and open the files either from the Finder or from Sourcetree. 
-Some document might be stored using Large File Storage (LFS) to save space on the repository. 
-Sourcetree can identify them automatically by using point and click: 
-repository, Git LFS, Pull LFS files
+Note that you can access and open the files either from the Finder or from Fork. 
+Some documents might be stored using Large File Storage (LFS) to save space on the repository. 
 
 ### Commit and Push
+
 Once you have made modifications on a file and saved them, it will appear in your `commit` window. 
 Here you can control one last time your file, write the commit message with the 
 issue reference (see below) and commit. 
-Once your commit is ready, you can `push` them to the origin/master repository.
+Once your commit is ready, you can `push` them to the origin/main repository.
 Note that you can click the "push immediately" box in the commit window 
 if you don't want to do it in two steps. 
-
-You can find more information on [commit and push](https://confluence.atlassian.com/sourcetreekb/commit-push-and-pull-a-repository-on-sourcetree-785616067.html)
 If you are working on a separate branch, 
-it is important to select this branch when pushing to origin/master.
+it is important to select this branch when pushing to origin/main.
 
 ## Issues and tests
 
-Please use the issues tracker on Bitbucket to identify any function-related issues.
+Please use the issues tracker on Github to identify any function-related issues.
 You can use these issues to track progress on the issue and 
 to comment or continue a conversation on that issue.
 Currently issue tracking is only open to those involved in the project.
@@ -101,9 +86,7 @@ in the commit description:
 Where the issue hash (i.e. #31) is preceded by
 `resolve`, `resolves`, `resolved`, `close`, `closes`, `closed`, `fix`, `fixes`, or `fixed`
 (capitalised or not),
-Bitbucket will automatically updated the status of the issue(s) mentioned.
-More details can be found [here](https://confluence.atlassian.com/bitbucket/resolve-issues-automatically-when-users-push-code-221451126.html).
-To set this up for Mac or Windows, see [this link](https://confluence.atlassian.com/sourcetreekb/link-to-bitbucket-issue-tracker-from-commits-296911608.html).
+Github will automatically updated the status of the issue(s) mentioned.
 
 Our current syntactical standard is to mention the issue first and then 
 provide a short description of what the committed changes do 
@@ -116,7 +99,7 @@ A final way of contributing to the package is in developing the
 vignettes/articles that illustrate the value added in the package. 
 Please contact me with any proposals here.
 
-Please note that the `roctopus` project is released with a 
+Please note that the `manynet` project is released with a 
 [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
 By contributing to this project, you agree to abide by its terms.
 

DESCRIPTION

@@ -1,8 +1,9 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Mark, and Map Myriad Networks
-Version: 0.4.4
-Date: 2024-03-15
-Description: A set of tools for making, modifying, marking, and mapping many different types of networks.
+Version: 1.0.0
+Date: 2024-06-23
+Description: Many tools for making, modifying, mapping, marking, measuring, 
+   and motifs and memberships of many different types of networks.
    All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
    and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
    The package includes functions for importing and exporting, creating and generating networks,
@@ -16,18 +17,22 @@ Language: en-GB
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
-Imports: 
+Imports:
     dplyr (>= 1.1.0),
     ggplot2,
     ggraph,
     igraph (>= 1.6.0),
     network,
     pillar,
-    tidygraph
-Suggests: 
+    tidygraph,
+    minMSE
+Suggests:
     BiocManager,
     concaveman,
+    future,
+    furrr,
     gganimate,
+    ggdendro,
     ggforce,
     gifski,
     graphlayouts,
@@ -36,18 +41,20 @@ Suggests:
     learnr,
     methods,
     migraph,
-    minMSE,
     multiplex,
+    netdiffuseR,
+    oaqc,
     patchwork,
     png,
     readxl,
     rmarkdown,
     roxygen2,
     RSiena,
+    sna,
     testthat (>= 3.0.0),
-    xml2,
-    future,
-    furrr
+    tibble,
+    tidyr,
+    xml2
 Enhances:
     Rgraphviz
 Authors@R: