Changed repository structure, removed GRaNIEdev, various small changes to...

Changed repository structure, removed GRaNIEdev, various small changes to code,  more changes and preparations follow

src/GRaNIE/DESCRIPTION

@@ -54,11 +54,7 @@ Imports:
     tibble,
     tidyselect,
     readr,
-    grid
-Depends:
-    R (>= 3.6),
-    tidyverse,
-    topGO,
+    grid,
     tidyr,
     dplyr,
     stats,
@@ -66,6 +62,10 @@ Depends:
     graphics,
     magrittr,
     tibble
+Depends:
+    R (>= 3.6),
+    tidyverse,
+    topGO
 Suggests:
     knitr,
     BSgenome.Hsapiens.UCSC.hg19,
@@ -95,5 +95,5 @@ License: LGPL (>= 3)
 LazyData: true
 URL: https://grp-zaugg.embl-community.io/GRaNIE
 BugReports: https://git.embl.de/grp-zaugg/GRaNIE/issues
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Config/testthat/edition: 3

src/GRaNIE/R/core.R

@@ -279,7 +279,11 @@ addData <- function(GRN, counts_peaks, normalization_peaks = "DESeq_sizeFactor",
     stopifnot(c("chr", "start", "end", "peakID", "isFiltered") %in% colnames(GRN@data$peaks$consensusPeaks))
     
     futile.logger::flog.info(paste0("Check for overlapping peaks..."))
-    consensus.gr   = .constructGRanges(GRN@data$peaks$consensusPeaks, seqlengths = .getChrLengths(genomeAssembly), GRN@config$parameters$genomeAssembly)
+    
+    # Assume 0-based exclusive format, see https://arnaudceol.wordpress.com/2014/09/18/chromosome-coordinate-systems-0-based-1-based/ and http://genome.ucsc.edu/FAQ/FAQformat.html#format1 for details
+    consensus.gr   = .constructGRanges(GRN@data$peaks$consensusPeaks, seqlengths = .getChrLengths(genomeAssembly), GRN@config$parameters$genomeAssembly, zeroBased = TRUE)
+    
+
     
     overlappingPeaks = which(GenomicRanges::countOverlaps(consensus.gr ,consensus.gr) >1)
     
@@ -4280,13 +4284,6 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
                                       background = "neighborhood", 
                                       clustering = "louvain",
                                       communities = seq_len(10), display = "byRank",
-                                      TF_rankType = "degree",
-                                      TF_topNodes_n = 0.1,
-                                      TF_names = NULL,
-                                      TF_plot_topn_pvalue = 30,
-                                      TF_plot_p = 0.05,
-                                      TF_plot_nSignificant = 3,
-                                      TF_plot_nGO = 10,
                                       outputFolder = NULL,
                                       forceRerun = FALSE) {
     
@@ -4310,17 +4307,6 @@ performAllNetworkAnalyses <- function(GRN, ontology = c("BP", "MF"),
     
     GRN = plotCommunitiesEnrichment(GRN, outputFolder = outputFolder, display = display, communities = communities, forceRerun = forceRerun)
     
-    
-    
-    GRN = calculateTFEnrichment(GRN, rankType = TF_rankType, n = TF_topNodes_n, TF.names = TF_names,
-                                            ontology = ontology, algorithm = algorithm, 
-                                            statistic = statistic, background = background,
-                                            forceRerun = forceRerun)
-    
-    GRN = plotTFEnrichment(GRN, rankType = TF_rankType, n = TF_topNodes_n, TF.names = TF_names,
-                           topn_pvalue = TF_plot_topn_pvalue, p = TF_plot_p, 
-                           nSignificant = TF_plot_nSignificant, nGO = TF_plot_nGO,
-                           outputFolder = outputFolder, forceRerun = forceRerun)
    
     
     .printExecutionTime(start)
@@ -4705,7 +4691,7 @@ calculateCommunitiesEnrichment <- function(GRN,
     communitiesDisplay = stats::na.omit(communitiesCount$community[communities])
   }
   
-  futile.logger::flog.info(paste0("Running enrichment analysis for all ", length(communitiesDisplay)," communities. This may take a while..."))
+  futile.logger::flog.info(paste0("Running enrichment analysis for all communities. This may take a while..."))
   
   mapping = .getGenomeObject(GRN@config$parameters$genomeAssembly, type = "packageName")
   

src/GRaNIE/R/helperFunctions.R

@@ -225,7 +225,9 @@
   
   
   if (nFilesToProcessTotal == 0) {
-    stop(paste0("No files to process in folder ", directory, " that fulfill the desired criteria (", patternCur, ")."))
+    message = paste0("No files to process in folder ", directory, " that fulfill the desired criteria (", patternCur, ").")
+    .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE)
+   
   } else {
     
     futile.logger::flog.info(paste0("The following", nFilesToProcessTotal, "files were found:\n", paste0(filesToProcess.vec, collapse = "\n ")))
@@ -385,25 +387,31 @@
   }
 }
 
-.constructGRanges <- function(annotation, seqlengths = NULL, genomeAssembly, stopIfError = TRUE, ...) {
+.constructGRanges <- function(annotation, seqlengths = NULL, genomeAssembly, zeroBased = TRUE, stopIfError = TRUE, ...) {
   
-  # Check if all start and end coordinates a
+  # Check if all start and end coordinates are valid
+  sharedErrorMessage = paste0("This should not happen and may indicate a wrong genome assembly version. Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates? ")
+    
+    
   invalidEnd = which(annotation$end > seqlengths[as.character(annotation$chr)] | annotation$end < 0)
   if (length(invalidEnd) > 0) {
-    futile.logger::flog.error(paste0(length(invalidEnd), " sequences have ends outside of the chromosome boundaries (e.g., sequences ", 
-                      paste0(invalidEnd[seq_len(min(5, length(invalidEnd)))], collapse = ","), "). This should not happen and may indicate a wrong genome assembly version. Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates?"))
-    stop()
+      
+      message = paste0(length(invalidEnd), " sequences have ends outside of the chromosome boundaries (e.g., sequences ", 
+                        paste0(invalidEnd[seq_len(min(5, length(invalidEnd)))], collapse = ","), ").", sharedErrorMessage)
+      
+      .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE)    
+   
   }
   
-  # Check if all start and end coordinates a
+  # Check if all start and end coordinates are valid and inside the chromosomes
   invalidStart = which(annotation$start > seqlengths[as.character(annotation$chr)] | annotation$start < 0)
   if (length(invalidStart) > 0) {
-    futile.logger::flog.error(paste0(length(invalidStart), " sequences have ends outside of the chromosome boundaries (e.g., sequences ", 
-                      paste0(invalidStart[seq_len(min(5, length(invalidStart)))], collapse = ","), "). This should not happen and may indicate a wrong genome assembly version. Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates?"))
-    stop()
+      message = paste0(length(invalidStart), " sequences have ends outside of the chromosome boundaries (e.g., sequences ", 
+                      paste0(invalidStart[seq_len(min(5, length(invalidStart)))], collapse = ","), ").", sharedErrorMessage)
+      .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE)    
   }
   
-  gr = GenomicRanges::makeGRangesFromDataFrame(annotation, keep.extra.columns = TRUE, seqinfo = seqlengths, ...)
+  gr = GenomicRanges::makeGRangesFromDataFrame(annotation, keep.extra.columns = TRUE, seqinfo = seqlengths, starts.in.df.are.0based = zeroBased, ...)
   
   # Check whether there are out-of-bound sequences, and abort if there are. This should not happen
   seq_outOfBound = which(end(gr) > seqlengths(gr)[as.character(GenomeInfoDb::seqnames(gr))])
@@ -412,13 +420,9 @@
       index = seq_len(min(length(seq_outOfBound),10))
       annotation_faultyEntries = paste0((GenomeInfoDb::seqnames(gr)[seq_outOfBound] %>% as.character())[index], ":", start(gr)[seq_outOfBound][index] , "-", end(gr)[seq_outOfBound][index], collapse = ",")
 
-      if (stopIfError ) {
-        futile.logger::flog.error(paste0(length(seq_outOfBound), " sequences are outside of the chromosome boundaries (e.g., ", annotation_faultyEntries, "). This should not happen and may indicate a wrong genome assembly version. Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates?"))
-        stop()
-      } else {
-        futile.logger::flog.warn(paste0(length(seq_outOfBound), " sequences are outside of the chromosome boundaries (e.g., ", annotation_faultyEntries, "). This should not happen and may indicate a wrong genome assembly version. Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates?"))
-        
-      }
+      message = paste0(length(seq_outOfBound), " sequences are outside of the chromosome boundaries (e.g., ", annotation_faultyEntries, "). This should not happen and may indicate either a wrong genome assembly version or that coordinates are not 0-based (see the Documentation). Check the validity of the input data and the parameters of the script. Are these really ", genomeAssembly, " coordinates?")
+      .checkAndLogWarningsAndErrors(NULL, message, isWarning = !stopIfError)
+      
       
   }
   

src/GRaNIE/R/plot.R

@@ -985,7 +985,7 @@ plotDiagnosticPlots_peakGene <- function(GRN,
   GRN = .addFunctionLogToObject(GRN)
   
   
-  # For compatibility reasons, re-crete the genes and peaks annotation if not present in the object
+  # For compatibility reasons, re-create the genes and peaks annotation if not present in the object
   if (! "peak.annotation" %in% colnames(GRN@annotation$consensusPeaks)) {
       GRN = .populatePeakAnnotation(GRN)
   }
@@ -1138,6 +1138,11 @@ plotDiagnosticPlots_peakGene <- function(GRN,
   nCur = length(xlabels_peakGene_r.class)
   xlabels_peakGene_r.class[setdiff(seq_len(nCur), c(1, floor(nCur/2), nCur))] <- ""
   
+  # For the last plot, which is wider, we label a few more
+  xlabels_peakGene_r.class2 = levels(peakGeneCorrelations.all$peak_gene.r.class)
+  nCur = length(xlabels_peakGene_r.class2)
+  xlabels_peakGene_r.class2[setdiff(seq_len(nCur), c(1, floor(nCur/4), floor(nCur/2), floor(nCur/4*3), nCur))] <- ""
+  
   xlabels_peakGene_praw.class = levels(peakGeneCorrelations.all$peak_gene.p.raw.class)
   nCur = length(xlabels_peakGene_praw.class)
   xlabels_peakGene_praw.class[setdiff(seq_len(nCur), c(1, floor(nCur/2), nCur))] <- ""
@@ -1246,7 +1251,9 @@ plotDiagnosticPlots_peakGene <- function(GRN,
               geom_bar(stat = "identity", position="dodge", na.rm = TRUE, width = 0.5) + 
               geom_hline(yintercept = 1, linetype = "dotted") + 
               xlab(xlabel) + ylab("Ratio") +
-              scale_fill_manual("Class", values = c(r_pos_class, dist_class), labels = c("real", "permuted", "r+ (r>0)", "r- (r<=0)")) + # labels vector can be kind of manually specified here because the levels were previosly defined in a certain order
+              scale_fill_manual("Class", values = c(dist_class, r_pos_class), 
+                                labels = c("real", "permuted", "r+ (r>0)", "r- (r<=0)"), 
+                                ) + # labels vector can be kind of manually specified here because the levels were previosly defined in a certain order
               scale_x_discrete(labels = xlabels_peakGene_praw.class) +
               theme_bw() +  
               #theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 8), strip.background = element_blank(), strip.placement = "outside", axis.title.y = element_blank()) +
@@ -1276,7 +1283,7 @@ plotDiagnosticPlots_peakGene <- function(GRN,
               geom_line(aes(peak_gene.r.class, nnorm, group = class, color= class), stat = "identity") +
               scale_fill_manual("Group", labels = names(dist_class), values = dist_class) +
               scale_color_manual("Group", labels = names(dist_class), values = dist_class) +
-              scale_x_discrete(labels = xlabels_peakGene_r.class, drop = FALSE) +
+              scale_x_discrete(labels = xlabels_peakGene_r.class2, drop = FALSE) +
               theme_bw() + theme(legend.position = "none") +
               xlab(xlabel) + ylab("Abundance") +
               theme_main  +
@@ -1312,10 +1319,15 @@ plotDiagnosticPlots_peakGene <- function(GRN,
       xlabel = paste0("Correlation raw\np-value (binned)")
       mainTitle = paste0("Summary QC (TF: ", TFCur, ", gene type: ", paste0(geneTypesSelected, collapse = "+"), ", ", .prettyNum(range), " bp promoter range)")
       
-      
-      allVars = c("peak.GC.class", "peak.annotation", "peak.width", "peak.mean","peak.median",
+      allVars = c("peak.GC.class",  "peak.width", "peak.mean","peak.median",
                   "peak.CV", "gene.median",  "gene.mean", "gene.CV", "peak.gene.combined.CV")
       
+      # If ChIPseeker is not installed, remove peak.annotation from it
+      if ("peak.annotation" %in% colnames(peakGeneCorrelations.all)) {
+          allVars = c(allVars, "peak.annotation")
+      }
+    
+      
       for (varCur in allVars) {
           #next
           # Save memory and prune the table and add only the variable we need here
@@ -2599,7 +2611,7 @@ plotTFEnrichment <- function(GRN, rankType = "degree", n = 0.1, TF.names = NULL,
     }
     
     # plot the comparative heatmap:
-    for (ontologyCur in names(purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results))){
+    for (ontology in names(purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results))){
       
       enrichmentData = purrr::transpose(purrr::transpose(GRN@stats$Enrichment[["byTF"]])$results)[[ontologyCur]][TFset]
       

src/GRaNIE/R/zzz.R

@@ -5,11 +5,7 @@
                      
                      "Welcome to the ", utils::packageName(), " package and thank you for using our software. This is ", utils::packageName(), " version ", utils::packageVersion(utils::packageName()),".\n",
                      
-                     "All project-related information, guidance, help, documentation and ways to contact us can be found here: https://grp-zaugg.embl-community.io/GRaNIE\n",
-                     
-                     "You may also check the R help\n"
-                     
-                     
+                     "All project-related information, guidance, help, documentation and ways to contact us can be found in the R help or here:\nhttps://grp-zaugg.embl-community.io/GRaNIE\n"
                      )
     
     packageStartupMessage(message)

src/GRaNIE/README.md

@@ -4,6 +4,13 @@ The companion packages *GRaNIE* (**G**ene **R**egul**a**tory **N**etwork **I**nf
 
 This page describes *GRaNIE*. For *GRaNPA*, please visit [this page](https://grp-zaugg.embl-community.io/GRaNPA).
 
+
+**Please use the following citation:**
+
+GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Neha Daga, Daria Nogina, Maksim Kholmatov, Nila Servaas, Sophia Mueller-Dott, Armando Reyes-Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B. Zaugg. bioRxiv 2021.12.18.473290; doi: https://doi.org/10.1101/2021.12.18.473290
+
+
+
 ### Summary
 
 *Towards a data-driven cell-type specific regulatory network including enhancers*

src/GRaNIE/_pkgdown.yml

@@ -17,10 +17,10 @@ navbar:
           desc: Bla
           href: articles/quickStart.html
           navbar: Test
-        - text: Introduction
-          desc: Learn what the GRaNIE package is and what you can use it for
-          navbar: Intro
-          href: articles/Introduction.html
+        - text: Package Details
+          desc: Learn what the GRaNIE package is and what you can use it for, including all methodological details
+          navbar: Methods
+          href: articles/packageDetails.html
         - text: Workflow example
           desc: Learn how to use the GRaNIE package with a full workflow example
           href: articles/workflow.html
@@ -36,11 +36,11 @@ articles:
   navbar: Getting started
   contents:
   - quickStart
-- title: Introduction
-  desc: Learn what the GRaNIE package is and what you can use it for
-  navbar: Introductory Vignette
+- title: Package Details
+  desc: Learn what the GRaNIE package is and what you can use it for, including all methodological details
+  navbar: Package Details
   contents:
-  - Introduction
+  - packageDetails
 - title: Workflow example
   desc: Learn how to use the GRaNIE package with a full workflow example
   navbar: Workflow Vignette

src/GRaNIE/docs/404.html

-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
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   gtag('js', new Date());
 
   gtag('config', 'G-530L9SXFM1');
 </script>
+</head>
+<body data-spy="scroll" data-target="#toc">
+    
 
-
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-title-body">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -80,14 +37,14 @@
         <span class="icon-bar"></span>
       </button>
       <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">GRaNIE</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.4</span>
+        <a class="navbar-link" href="index.html">GRaNIEdev</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.4</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
-        <li>
+<li>
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 </li>
 <li>
@@ -100,11 +57,11 @@
     <span class="caret"></span>
   </a>
   <ul class="dropdown-menu" role="menu">
-    <li>
+<li>
       <a href="articles/quickStart.html">Getting Started</a>
     </li>
     <li>
-      <a href="articles/Introduction.html">Introduction</a>
+      <a href="articles/packageDetails.html">Package Details</a>
     </li>
     <li>
       <a href="articles/workflow.html">Workflow example</a>
@@ -118,19 +75,17 @@
   <a href="news/index.html">Changelog &amp; News</a>
 </li>
       </ul>
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+<ul class="nav navbar-nav navbar-right"></ul>
+</div>
+<!--/.nav-collapse -->
+  </div>
+<!--/.container -->
+</div>
+<!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="contents col-md-9">
     <div class="page-header">
       <h1>Page not found (404)</h1>
@@ -141,31 +96,31 @@ Content not found. Please use links in the navbar.
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-    <nav id="toc" data-toggle="toc" class="sticky-top">
-      <h2 data-toc-skip>Contents</h2>
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
     </nav>
-  </div>
+</div>
 
 </div>
 
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
+      <footer><div class="copyright">
+  <p></p>
+<p>Developed by Christian Arnold, Judith Zaugg, Rim Moussa.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
 </div>
 
       </footer>
-   </div>
+</div>
 
   
 
 
+  
+
   </body>
 </html>
-
-

src/GRaNIE/docs/articles/Introduction_files/header-attrs-2.11/header-attrs.js

-// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
-// be compatible with the behavior of Pandoc < 2.8).
-document.addEventListener('DOMContentLoaded', function(e) {
-  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
-  var i, h, a;
-  for (i = 0; i < hs.length; i++) {
-    h = hs[i];
-    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
-    a = h.attributes;
-    while (a.length > 0) h.removeAttribute(a[0].name);
-  }
-});

src/GRaNIE/docs/articles/index.html

-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Articles • GRaNIE</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
-
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
-
-<!-- bootstrap-toc -->
-<link rel="stylesheet" href="../bootstrap-toc.css">
-<script src="../bootstrap-toc.js"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Articles" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Articles • GRaNIEdev</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
-<!-- Global site tag (gtag.js) - Google Analytics -->
-<script async src="https://www.googletagmanager.com/gtag/js?id=G-530L9SXFM1"></script>
-<script>
+<![endif]--><!-- Global site tag (gtag.js) - Google Analytics --><script async src="https://www.googletagmanager.com/gtag/js?id=G-530L9SXFM1"></script><script>
   window.dataLayer = window.dataLayer || [];
   function gtag(){dataLayer.push(arguments);}
   gtag('js', new Date());
 
   gtag('config', 'G-530L9SXFM1');
-</script>
-
+</script></head><body data-spy="scroll" data-target="#toc">
+    
 
-  </head>
-
-  <body data-spy="scroll" data-target="#toc">
     <div class="container template-article-index">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -80,14 +22,13 @@
         <span class="icon-bar"></span>
       </button>
       <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">GRaNIE</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.14.4</span>
+        <a class="navbar-link" href="../index.html">GRaNIEdev</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.14.4</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
+      <ul class="nav navbar-nav"><li>
   <a href="../index.html"></a>
 </li>