Merge pull request #72 from jhollway/develop

Framework changes

Author: jhollway

.Rbuildignore

@@ -4,3 +4,6 @@
 ^\.Rproj\.user$
 ^working$
 ^\.github$
+^data-raw$
+^docs$
+^pkgdown$

.github/workflows/prchecks.yml

@@ -16,7 +16,7 @@ jobs:
         config:
           - {os: macOS-latest,   r: 'release', artifact_name: '*.tar.gz', asset_name: macOS}
           - {os: windows-latest, r: 'release', artifact_name: '*.zip', asset_name: winOS}
-          # - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", artifact_name: '*.tar.gz', asset_name: linuxOS}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", artifact_name: '*.tar.gz', asset_name: linuxOS}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -46,22 +46,23 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      #- name: Install system dependencies
-      #  if: runner.os == 'Linux'
-      #  env:
-      #    RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-      #  run: |
-      #    Rscript -e "remotes::install_github('r-hub/sysreqs')"
-      #    sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-      #    sudo -s eval "$sysreqs"
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("pkgbuild")
         shell: Rscript {0}
+
       - name: Document
         run: Rscript -e 'roxygen2::roxygenise()'
+
       - name: Binary
         run: |
           pkgbuild::clean_dll()

.github/workflows/pushrelease.yml

@@ -118,7 +118,7 @@ jobs:
         run: ls -R
 
       - name: Rename Mac release
-        run: mv ./macOS/*.tgz roctopus_macOS.tgz 
+        run: mv ./macOS/*.tgz migraph_macOS.tgz 
 
       - name: Upload Mac binary
         id: upload-mac
@@ -127,12 +127,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: roctopus_macOS.tgz
-          asset_name: roctopus_macOS.tgz
+          asset_path: migraph_macOS.tgz
+          asset_name: migraph_macOS.tgz
           asset_content_type: application/zip
 
       - name: Rename Linux release
-        run: mv ./linuxOS/*.tar.gz roctopus_linuxOS.tar.gz 
+        run: mv ./linuxOS/*.tar.gz migraph_linuxOS.tar.gz 
 
       - name: Upload Linux binary
         id: upload-lin
@@ -141,12 +141,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: roctopus_linuxOS.tar.gz
-          asset_name: roctopus_linuxOS.tar.gz
+          asset_path: migraph_linuxOS.tar.gz
+          asset_name: migraph_linuxOS.tar.gz
           asset_content_type: application/zip
 
       - name: Rename Windows release
-        run: mv ./winOS/*.zip roctopus_winOS.zip 
+        run: mv ./winOS/*.zip migraph_winOS.zip 
 
       - name: Upload Windows binary
         id: upload-win
@@ -155,6 +155,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps
-          asset_path: roctopus_winOS.zip
-          asset_name: roctopus_winOS.zip
+          asset_path: migraph_winOS.zip
+          asset_name: migraph_winOS.zip
           asset_content_type: application/zip          

.gitignore

@@ -6,3 +6,4 @@ inst/doc
 *.Rd
 data-raw/*
 docs/
+working/*

DESCRIPTION

@@ -6,7 +6,7 @@ Description: This package assembles a number of utility functions for
 URL: https://github.com/jhollway/migraph
 BugReports: https://github.com/jhollway/migraph/issues
 Depends: R (>= 3.4.0)
-License: MIT
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

NAMESPACE

@@ -1,37 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
-export(centrality_betweenness)
-export(centrality_closeness)
-export(centrality_degree)
-export(col_project)
+export(as_incidence_matrix)
 export(create_chain)
 export(create_match)
 export(create_nest)
 export(create_silos)
-export(df_to_mat)
-export(netlm2)
 export(play_twomode)
-export(plot_2x2)
-export(plot_globalnet)
-export(plot_multilevel)
-export(plot_twomode)
-export(project_list)
-export(row_project)
-export(threemode_clustering)
-export(twomode_2x2)
-export(twomode_centrality_degree)
-export(twomode_centralization_betweeness)
-export(twomode_centralization_closeness)
-export(twomode_centralization_degree)
-export(twomode_clustering)
-export(twomode_coherence)
-export(twomode_components)
-export(twomode_constraint)
-export(twomode_dominance)
-export(twomode_modularity)
-export(twomode_smallworld)
-import(geosphere)
-import(ggplot2)
-import(igraph)
-import(threejs)
-import(tidyverse)
+export(project_cols)
+export(project_rows)
+importFrom(igraph,as.igraph)
+importFrom(igraph,as_adjacency_matrix)
+importFrom(igraph,bipartite.projection)
+importFrom(igraph,graph_from_incidence_matrix)
+importFrom(tidygraph,as_tbl_graph)
+importFrom(tidygraph,is.tbl_graph)
+importFrom(tidygraph,play_bipartite)

NEWS.md

@@ -1,18 +1,17 @@
 # migraph 0.4.0
 
-2020-12-21
+2021-01-08
 
 ## Package
 
 * Package name change from roctopus to `{migraph}`
+  * Closed #50 with new logo
+* Now builds Linux binary too
 
-## Analysis
+## Manipulation
 
-* Added `centrality_degree()` to mask tidygraph function with correctly normalised two-mode calculation
-* Added `centrality_closeness()` to mask tidygraph function with correctly normalised two-mode calculation
-* Added `centrality_betweenness()` to mask tidygraph function with correctly normalised two-mode calculation
-* Renamed `twomode_centralization_between()` to `twomode_centralization_betweenness()`
-* Added `twomode_centralization_closeness()`
+* Added `project_rows()` and `project_cols()` to make it easier to project two-mode networks in different formats (matrix, igraph, tidygraph) into projected versions in the same format
+* Closed #30 with conversion from different data frame formats, e.g. weighted and unweighted edgelists, into an incidence matrix with `as_incidence_matrix()`
 
 ## Data