Style checks and fixes

.Rbuildignore

@@ -5,3 +5,6 @@
 ^appveyor\.yml$
 ^doc$
 ^Meta$
+^\.github$
+^\.lintr
+^docs$

.github/workflows/build.yml

@@ -50,7 +50,6 @@ jobs:
         with:
           extra-packages: |
             any::devtools
-            any::covr
 
       - name: Document
         run: devtools::document()
@@ -62,14 +61,10 @@ jobs:
           git config --local user.name "$GITHUB_ACTOR"
           git config --local user.email "[email protected]"
           git add man/\* NAMESPACE
-          git commit -m "Update documentation" || echo "No changes to commit"
+          git commit -m "Update documentation (bot)" || echo "No changes to commit"
           git pull --ff-only
           git push origin
 
-      - name: Check package
+      - name: Check package with devtools
         run: devtools::check()
         shell: Rscript {0}
-
-      - name: Check coverage
-        run: covr::codecov(quiet = FALSE)
-        shell: Rscript {0}

.github/workflows/quality.yaml

@@ -0,0 +1,40 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: Quality checks
+
+jobs:
+  lint-project:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::covr
+            any::lintr
+            any::styler
+
+      - name: Styler
+        run: styler::style_pkg(filetype = c('R', 'Rprofile', 'Rmd'), dry='fail')
+        shell: Rscript {0}
+
+      - name: Lintr
+        run: lintr::lint_package()
+        shell: Rscript {0}
+
+      - name: Coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}

.lintr

@@ -0,0 +1,7 @@
+error_on_lint: TRUE
+linters: with_defaults(
+    open_curly_linter = NULL,
+    closed_curly_linter = NULL,
+    spaces_left_parentheses_linter = NULL,
+    seq_linter = NULL
+  )

NAMESPACE

@@ -49,17 +49,17 @@ export(min_emd_exhaustive)
 export(min_emd_optimise)
 export(min_emd_optimise_fast)
 export(netdis)
-export(netdis.plot)
 export(netdis_centred_graphlet_counts)
 export(netdis_expected_counts)
 export(netdis_many_to_many)
 export(netdis_one_to_many)
 export(netdis_one_to_one)
+export(netdis_plot)
 export(netdis_subtract_exp_counts)
 export(netdis_uptok)
-export(netemd.plot)
 export(netemd_many_to_many)
 export(netemd_one_to_one)
+export(netemd_plot)
 export(netemd_single_pair)
 export(normalise_dhist_mass)
 export(normalise_dhist_variance)

R/PlottingFunctions.R

@@ -1,56 +1,108 @@
 
 #' Heatmap of Netdis many-to-many comparisons
 #'
-#' Provides a heatmap and dendrogram for the network comparisons via \code{pheatmap}.
-#' 
+#' Provides a heatmap and dendrogram for the network comparisons via
+#' \code{pheatmap}.
+#'
 #' @param netdislist Default output of \code{netdis_many_to_many}.
 #'
-#' @param whatrow Selection of the row in \code{netdis_many_to_many$comp_spec} to be used for plotting.
+#' @param whatrow Selection of the row in \code{netdis_many_to_many$comp_spec}
+#' to be used for plotting.
 #'
-#' @param clustering_method Clustering method as allowed in the \code{pheatmap} function from the \code{pheatmap} package. The dendrogram will appear if \code{docluster} is TRUE (default).
+#' @param clustering_method Clustering method as allowed in the \code{pheatmap}
+#' function from the \code{pheatmap} package. The dendrogram will appear if
+#' \code{docluster} is TRUE (default).
 #'
 #' @param main Title of the plot.
-#' 
-#' @param docluster controls the order of the rows and columns. If TRUE (default) the rows and columns will be reordered to create the dendrogram. If FALSE, then only the heatmap is drawn.
-#' 
-#' @return Provides a heatmap and dendrogram for the network comparisons via \code{pheatmap}.
+#'
+#' @param docluster controls the order of the rows and columns. If TRUE
+#' (default) the rows and columns will be reordered to create the dendrogram. If
+#' FALSE, then only the heatmap is drawn.
+#'
+#' @return Provides a heatmap and dendrogram for the network comparisons via
+#' \code{pheatmap}.
 #' @export
 
-netdis.plot <- function(netdislist,whatrow=c(1,2)[2],clustering_method="ward.D",main="Nedis",docluster=TRUE){
-  adjmat <- cross_comp_to_matrix(measure = netdislist$netdis[whatrow,], cross_comparison_spec = netdislist$comp_spec)
+netdis_plot <- function(netdislist,
+                        whatrow = c(1, 2)[2],
+                        clustering_method = "ward.D",
+                        main = "Nedis",
+                        docluster = TRUE) {
+  adjmat <- cross_comp_to_matrix(
+    measure = netdislist$netdis[whatrow, ],
+    cross_comparison_spec = netdislist$comp_spec
+  )
   vnames <- rownames(adjmat)
-
-  legend1 <- seq(min(adjmat),max(adjmat),length.out = 5)
-  levels1 <- round(legend1,digits = 2)
-  pheatmap::pheatmap(mat = as.dist(adjmat),cluster_rows = docluster,cluster_cols = docluster,clustering_method = clustering_method,angle_col=45,main = main,treeheight_row = 80,labels_row = vnames,labels_col = vnames,display_numbers = TRUE,legend_breaks = legend1,legend_labels = levels1)
+
+  legend1 <- seq(min(adjmat), max(adjmat), length.out = 5)
+  levels1 <- round(legend1, digits = 2)
+  pheatmap::pheatmap(
+    mat = stats::as.dist(adjmat),
+    cluster_rows = docluster,
+    cluster_cols = docluster,
+    clustering_method = clustering_method,
+    angle_col = 45,
+    main = main,
+    treeheight_row = 80,
+    labels_row = vnames,
+    labels_col = vnames,
+    display_numbers = TRUE,
+    legend_breaks = legend1,
+    legend_labels = levels1
+  )
 }
 
 
 
 
 #' Heatmap of NetEmd many-to-many comparisons
 #'
-#' Provides a heatmap and dendrogram for the network comparisons via \code{pheatmap}.
-#' 
+#' Provides a heatmap and dendrogram for the network comparisons via
+#' \code{pheatmap}.
+#'
 #' @param netdislist Default output of \code{netdis_many_to_many}.
 #'
-#' @param whatrow Selection of the row in \code{netdis_many_to_many$comp_spec} to be used for plotting.
+#' @param whatrow Selection of the row in \code{netdis_many_to_many$comp_spec}
+#' to be used for plotting.
 #'
-#' @param clustering_method Clustering method as allowed in the \code{pheatmap} function from the \code{pheatmap} package. The dendrogram will appear if \code{docluster} is TRUE (default).
+#' @param clustering_method Clustering method as allowed in the \code{pheatmap}
+#' function from the \code{pheatmap} package. The dendrogram will appear if
+#' \code{docluster} is TRUE (default).
 #'
 #' @param main Title of the plot.
-#' 
-#' @param docluster controls the order of the rows and columns. If TRUE (default) the rows and columns will be reordered to create the dendrogram. If FALSE, then only the heatmap is drawn.
-#' 
-#' @return Provides a heat map and dendrogram for the network comparisons via \code{pheatmap}.
+#'
+#' @param docluster controls the order of the rows and columns. If TRUE
+#' (default) the rows and columns will be reordered to create the dendrogram. If
+#' FALSE, then only the heatmap is drawn.
+#'
+#' @return Provides a heat map and dendrogram for the network comparisons via
+#' \code{pheatmap}.
 #' @export
 
-netemd.plot <- function(netemdlist,clustering_method="ward.D",main="NetEmd",docluster=TRUE){
-  adjmat <- cross_comp_to_matrix(measure = netemdlist$netemds, cross_comparison_spec = netemdlist$comp_spec)
+netemd_plot <- function(netemdlist,
+                        clustering_method = "ward.D",
+                        main = "NetEmd",
+                        docluster = TRUE) {
+  adjmat <- cross_comp_to_matrix(
+    measure = netemdlist$netemds,
+    cross_comparison_spec = netemdlist$comp_spec
+  )
   vnames <- rownames(adjmat)
-
-  legend1 <- seq(min(adjmat),max(adjmat),length.out = 5)
-  levels1 <- round(legend1,digits = 2)
-  pheatmap::pheatmap(mat = as.dist(adjmat),cluster_rows = docluster,cluster_cols = docluster,clustering_method = clustering_method,angle_col=45,main = main,treeheight_row = 80,labels_row = vnames,labels_col = vnames,display_numbers = TRUE,legend_breaks = legend1,legend_labels = levels1)
-
+
+  legend1 <- seq(min(adjmat), max(adjmat), length.out = 5)
+  levels1 <- round(legend1, digits = 2)
+  pheatmap::pheatmap(
+    mat = stats::as.dist(adjmat),
+    cluster_rows = docluster,
+    cluster_cols = docluster,
+    clustering_method = clustering_method,
+    angle_col = 45,
+    main = main,
+    treeheight_row = 80,
+    labels_row = vnames,
+    labels_col = vnames,
+    display_numbers = TRUE,
+    legend_breaks = legend1,
+    legend_labels = levels1
+  )
 }

R/RcppExports.R

@@ -12,7 +12,7 @@ counts_from_observations <- function(features) {
 }
 
 #' @title
-#' Compute Earth Mover's Distance (EMD) between two Empirical Cumulative 
+#' Compute Earth Mover's Distance (EMD) between two Empirical Cumulative
 #' Density Functions (ECDFs)
 #'
 #' @param locations1 Locations for ECDF 1
@@ -22,6 +22,11 @@ counts_from_observations <- function(features) {
 #'
 #' @export
 emd_fast_no_smoothing <- function(locations1, values1, locations2, values2) {
-    .Call(`_netdist_emd_fast_no_smoothing`, locations1, values1, locations2, values2)
+    .Call(
+        `_netdist_emd_fast_no_smoothing`,
+        locations1,
+        values1,
+        locations2,
+        values2
+    )
 }
-

R/data.R

@@ -36,9 +36,17 @@
 #' }
 #'
 #' @format A list of \code{igraph} objects.
-#' @source \strong{PPI data (EBV, HSV-1, KSHV, VZV):} Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, et al. (2009) Evolutionarily Conserved Herpesviral Protein Interaction Networks. PLoS Pathog 5(9): e1000570. \url{https://doi.org/10.1371/journal.ppat.1000570}. Data from Table S2 in the supporting information.
-#' @source \strong{PPI data (ECL):} Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J (2009) The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol 5(10): e1000523. \url{https://doi.org/10.1371/journal.pcbi.1000523}
-#' @source \strong{Taxonomy ground truth:} NCBI taxonomy database. \url{https://www.ncbi.nlm.nih.gov/taxonomy}
+#' @source \strong{PPI data (EBV, HSV-1, KSHV, VZV):} Fossum E, Friedel CC,
+#' Rajagopala SV, Titz B, Baiker A, Schmidt T, et al. (2009) Evolutionarily
+#' Conserved Herpesviral Protein Interaction Networks. PLoS Pathog 5(9):
+#' e1000570. \url{https://doi.org/10.1371/journal.ppat.1000570}. Data from Table
+#' S2 in the supporting information.
+#' @source \strong{PPI data (ECL):} Peregrín-Alvarez JM, Xiong X, Su C,
+#' Parkinson J (2009) The Modular Organization of Protein Interactions in
+#' Escherichia coli. PLoS Comput Biol 5(10): e1000523.
+#' \url{https://doi.org/10.1371/journal.pcbi.1000523}
+#' @source \strong{Taxonomy ground truth:} NCBI taxonomy database.
+#' \url{https://www.ncbi.nlm.nih.gov/taxonomy}
 #' @encoding UTF-8
 "virusppi"
 
@@ -47,18 +55,29 @@
 
 
 #' World trade networks from 1985–2014
-#' 
-#' The world trade data set consists of a small sample of world trade networks for the years 2001-2014, and pre-computed subgraph counts of a larger set of world trade networks (1985–2014). The world trade networks are based on the data set from [Feenstra et al., 2005] for the years 1962- 2000 and on the United Nations division COMTRADE [Division, 2015] for the years 2001-2014.
+#'
+#' The world trade data set consists of a small sample of world trade networks
+#' for the years 2001-2014, and pre-computed subgraph counts of a larger set of
+#' world trade networks (1985–2014). The world trade networks are based on the
+#' data set from [Feenstra et al., 2005] for the years 1962- 2000 and on the
+#' United Nations division COMTRADE [Division, 2015] for the years 2001-2014.
 #'
 #' \itemize{
-#'  \item wtnets:  List of \code{igraph} objects providing the world trade networks from 2001–2014.
-#'  \item Counts:  Pre-computed graphlet counts for the world trade networks in the years 1985-2014.
+#'  \item wtnets:  List of \code{igraph} objects providing the world trade
+#'  networks from 2001–2014.
+#'  \item Counts:  Pre-computed graphlet counts for the world trade networks in
+#'  the years 1985-2014.
 #'  }
-#'  
-#' @format A list of two elements. The first element, 'wtnets', is a list of \code{igraph} objects providing a small sample of world trade networks from 2001–2014. The second element, 'Counts', is a list of pre-computed subgraph counts of world trade networks in the years 1985-2014.
-#' @source \strong{World trade networks:}. United nations commodity trade statistics database (UN comtrade). http://comtrade.un.org/, 2015.
-#' @source \strong{Subgraph Counts:} Feenstra RC,Lipsey RE, Deng H, Ma AC, and Mo H. (2005) World trade flows: 1962-2000. Technical report, National Bureau of Economic Research. (See also https://cid.econ.ucdavis.edu/wix.html).
-#' 
+#'
+#' @format A list of two elements. The first element, 'wtnets', is a list of
+#' \code{igraph} objects providing a small sample of world trade networks from
+#' 2001–2014. The second element, 'Counts', is a list of pre-computed subgraph
+#' counts of world trade networks in the years 1985-2014.
+#' @source \strong{World trade networks:}. United nations commodity trade
+#' statistics database (UN comtrade). http://comtrade.un.org/, 2015.
+#' @source \strong{Subgraph Counts:} Feenstra RC,Lipsey RE, Deng H, Ma AC, and
+#' Mo H. (2005) World trade flows: 1962-2000. Technical report, National Bureau
+#' of Economic Research. (See also https://cid.econ.ucdavis.edu/wix.html).
+#'
 #' @encoding UTF-8
 "worldtradesub"
-