Update NAMESPACE and .Rd files

NAMESPACE

@@ -1,8 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BinaryDomainNetwork)
 export(GCA2Lineage)
-export(GenContextNetwork)
 export(IPG2Lineage)
 export(acc2FA)
 export(acc2Lineage)
@@ -29,32 +27,34 @@ export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
 export(countByColumn)
+export(createBinaryDomainNetwork)
+export(createDomainNetwork)
 export(createFA2Tree)
+export(createGenomicContextNetwork)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createMSA_Kalign)
+export(createMSA_PDF)
 export(createRepresentativeAccNum)
+export(createUndirectedGenomicContextNetwork)
 export(createWordCloud2Element)
 export(createWordCloudElement)
 export(create_lineage_lookup)
-export(domain_network)
 export(downloadAssemblySummary)
 export(efetchIPG)
 export(extractAccNum)
 export(filterByDomains)
 export(filterByFrequency)
 export(findParalogs)
 export(formatJobArgumentsHTML)
-export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_msa)
 export(getAccNumFromFA)
 export(getTopAccByLinDomArch)
 export(get_proc_medians)
 export(get_proc_weights)
 export(make_opts2procs)
 export(mapAcc2Name)
 export(map_advanced_opts2procs)
-export(msa_pdf)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)
 export(plotLineageDA)