1.4.0 release

.gitignore

@@ -1,18 +1,23 @@
-.Rproj.user
+*.ASOIAF.ged
+*.Rproj
+*.knit.md
 .DS_Store
-data-raw/ASOIAF.ged
-R/.Rhistory
+.Rdata
 .Rhistory
-paper/paper.html
+.Rproj.user
+.httr-oauth
+.quarto
+.vscode/launch.json
 /Meta/
-*.knit.md
-vignettes/articles/paper.html
 BGmisc.code-workspace
-tests/testthat/Rplots.pdf
-*.ASOIAF.ged
-ASOIAF.ged
-*.Rproj
-
-.vscode/launch.json
-dataRelatedPairs_new2.csv
+R/.Rhistory
+benchmark_results.csv
+data-raw/ASOIAF.ged
 data-raw/ASOIAF_040725.ged
+dataRelatedPairs.csv
+dataRelatedPairs_new2.csv
+paper/paper.html
+tests/testthat/Rplots.pdf
+vignettes/articles/paper.html
+.vscode/settings.json
+data-raw/logo_orange.png

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BGmisc
 Title: An R Package for Extended Behavior Genetics Analysis
-Version: 1.3.5.1
+Version: 1.4.0
 Authors@R: c(
     person("S. Mason", "Garrison", , "garrissm@wfu.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4804-6003")),

NAMESPACE

@@ -1,25 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
 export(SimPed)
-export(allGens)
+export(assignCoupleIDs)
+export(buildTreeGrid)
+export(calcAllGens)
+export(calcFamilySize)
 export(calculateRelatedness)
 export(checkIDs)
 export(checkParentIDs)
 export(checkPedigreeNetwork)
 export(checkSex)
 export(com2links)
 export(comp2vech)
+export(computeParentAdjacency)
 export(createGenDataFrame)
 export(dropLink)
 export(evenInsert)
-export(extractSummaryText)
-export(famSizeCal)
 export(fitComponentModel)
+export(getWikiTreeSummary)
 export(identifyComponentModel)
 export(inferRelatedness)
+export(insertEven)
 export(makeInbreeding)
 export(makeTwins)
-export(parseTree)
 export(ped2add)
 export(ped2ce)
 export(ped2cn)
@@ -30,18 +33,24 @@ export(ped2maternal)
 export(ped2mit)
 export(ped2paternal)
 export(plotPedigree)
+export(readGed)
 export(readGedcom)
 export(readWikifamilytree)
+export(readgedcom)
 export(recodeSex)
 export(related_coef)
-export(relatedness)
 export(repairSex)
 export(resample)
 export(simulatePedigree)
+export(summariseFamilies)
+export(summariseMatrilines)
+export(summarisePatrilines)
+export(summarisePedigrees)
 export(summarizeFamilies)
 export(summarizeMatrilines)
 export(summarizePatrilines)
 export(summarizePedigrees)
+export(traceTreePaths)
 export(vech)
 import(data.table)
 import(kinship2)

NEWS.md

@@ -1,7 +1,14 @@
-# BGmisc 1.3.6
+# BGmisc 1.4.0
 * revived checkParents function to check for handling phantom parents and missing parents
 * added tests for checkParents function
 * added GoT analysis
+* reduced complexity of com2links, summarizePedigree, and checkIDs with the use of subfunctions
+* allow verbose argument to be passed to standardizeColnames
+* list SimPed and related_coef as aliases for functions
+* harmonizing function names like calcFamilySize from famSizeCal
+* implemented adjBeta function to evaluation alternative build method
+* reorganize file names to be more consistent
+* harmonized famID
 
 # BGmisc 1.3.5.1
 * Setting the default for the `sparse` argument in `ped2com()` to TRUE