Added factor analysis to dna_cluster and renamed dna_plotMDS to dna_p…

…lotCoordinates

Update rDNA package.R

@@ -0,0 +1,115 @@
+# how to write an R package https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
+
+library("devtools")
+library("roxygen2")
+
+#Update Documentation
+#setwd("C:/Users/binis/Documents/GitHub/dna/rDNA")
+#setwd("F:/Dropbox/Github/dna/rDNA")
+# setwd("/home/johannes/Documents/Github 4/dna/rDNA/")
+setwd("/home/johannes/Documents/Github/dna/rDNA/")
+desc <- readLines("DESCRIPTION")
+date <- desc[grepl("^Date:", desc)]
+date2 <- gsub("[^[:digit:]-]", "", date)
+desc[grepl("^Date:", desc)] <- gsub(date2, Sys.Date(), desc[grepl("^Date:", desc)])
+vers <- desc[grepl("^Version:", desc)]
+vers2 <- gsub("[^[:digit:].]", "", vers)
+vers3 <- readline(prompt = paste("New Version? Old:", vers2)) 
+desc[grepl("^Version:", desc)] <- gsub(vers2, vers3, desc[grepl("^Version:", desc)])
+writeLines(desc, "DESCRIPTION")
+
+
+roxygen2::roxygenise(clean = TRUE)
+setwd("..")
+devtools::check("rDNA")
+devtools::spell_check("rDNA", dict = "en_GB", ignore = c(
+  "CLASSPATH",
+  "dd",
+  "dna",
+  "DNA's",
+  "docTitle",
+  "excludeTypes",
+  "Gruber",
+  "Leifeld",
+  "igraph",
+  "ggplot",
+  "java",
+  "Jaccard",
+  "etc",
+  "mySQL",
+  "nw",
+  "org",
+  "pts",
+  "wd",
+  "plottable",
+  "linetype",
+  "bw", 
+  "color", 
+  "cutree", 
+  "eigen", 
+  "lineend", 
+  "louvain", 
+  "mcquitty", 
+  "MDS", 
+  "pam", 
+  "plotDendro", 
+  "RColorBrewer", 
+  "walktrap", 
+  "yyyy",
+  "onemode",
+  "twomode",
+  "getDocuments",
+  "clust",
+  "dh",
+  "drl",
+  "graphopt",
+  "kk",
+  "knitr",
+  "lables",
+  "lgl",
+  "mds",
+  "POSIXct",
+  "qualifierAggregation",
+  "setDocuments",
+  "dist",
+  "edgelist",
+  "eventSequence",
+  "isoMDS",
+  "plotMDS",
+  "timewindow",
+  "vegdist"
+))
+#source("https://install-github.me/MangoTheCat/goodpractice")
+#goodpractice::gp("rDNA")
+#lintr::lint("rDNA.R")
+#lintr::lint_package("rDNA")
+
+#devtools::install("rDNA")
+
+# update github
+system("git status")
+
+system("git add -A")
+commit_message <- readline(prompt = "Commit message") 
+system(paste0("git commit -m'",
+              commit_message,
+              "'"))
+
+#build
+build(pkg = "rDNA", manual = TRUE)
+
+# create the package in wd
+setwd("C:/Users/binis/Documents/GitHub/dna")
+install("rDNA", args = c("--no-multiarch", "--no-test-load"))
+
+# change version number in manual
+
+
+
+### quick test
+setwd("/home/johannes/Documents/Github/dna/rDNA/")
+roxygen2::roxygenise(clean = TRUE)
+setwd("..")
+#devtools::check("rDNA")
+devtools::install("rDNA")
+

rDNA/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rDNA
-Version: 2.0.82
-Date: 2018-05-20
+Version: 2.0.83
+Date: 2018-05-21
 Title: Discourse Network Analysis in R
 Authors@R: 
     c(person("Philip", "Leifeld", email = "Philip.Leifeld@glasgow.ac.uk", 

rDNA/NAMESPACE

@@ -12,11 +12,11 @@ export(dna_getDocuments)
 export(dna_gui)
 export(dna_init)
 export(dna_network)
+export(dna_plotCoordinates)
 export(dna_plotDendro)
 export(dna_plotFrequency)
 export(dna_plotHeatmap)
 export(dna_plotHive)
-export(dna_plotMDS)
 export(dna_plotNetwork)
 export(dna_plotTimeWindow)
 export(dna_removeDocument)
@@ -65,6 +65,7 @@ importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,dendrapply)
 importFrom(stats,dist)
+importFrom(stats,factanal)
 importFrom(stats,hclust)
 importFrom(stats,is.leaf)
 importFrom(stats,kmeans)