Temporal

.gitignore

@@ -58,3 +58,13 @@ vignettes/understanding_relatedness.Xmd
 .positai
 *.tmp.*
 benchmark_rowlessParents_results.csv
+dev/*
+fit_ace0_100_500_.rds
+fit_ace_linear_100_500_.rds
+fit_ace_linear_h_100_500_.rds
+fit_ae0_100_500_.rds
+fit_ae_linear_100_500_.rds
+fit_ae_linear_h_100_500_.rds
+fit_mace0_100_500_.rds
+fit_mace_linear_100_500_.rds
+fit_mace_linear_h_100_500_.rds

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BGmisc
 Title: An R Package for Extended Behavior Genetics Analysis
-Version: 1.9.0
+Version: 1.9.0.9
 Authors@R: c(
     person("S. Mason", "Garrison", , "garrissm@wfu.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4804-6003")),
@@ -58,5 +58,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Config/roxygen2/version: 8.0.0
-RoxygenNote: 8.0.0
+Config/roxygen2/version: 8.1.0

NAMESPACE

@@ -9,9 +9,15 @@ export(addPaternalChain)
 export(addPaternalLineFlag)
 export(alignPhenToMatrix)
 export(buildFamilyGroups)
+export(buildFamilyGroups_list)
 export(buildOneFamilyGroup)
+export(buildOneTemporalFamilyGroup)
 export(buildPedigreeModelCovariance)
 export(buildPedigreeMx)
+export(buildTemporalFamilyGroups)
+export(buildTemporalFamilyGroups_list)
+export(buildTemporalPedigreeModelCovariance)
+export(buildTemporalPedigreeMx)
 export(buildTreeGrid)
 export(calcAllGens)
 export(calcFamilySize)
@@ -30,6 +36,7 @@ export(dropLink)
 export(findLeaves)
 export(fitComponentModel)
 export(fitPedigreeModel)
+export(fitTemporalPedigreeModel)
 export(getGenDist)
 export(getWikiTreeSummary)
 export(identifyComponentModel)
@@ -75,14 +82,20 @@ export(summarizePedigrees)
 export(traceTreePaths)
 export(trimPedigree)
 export(vech)
-importFrom(Matrix,Diagonal)
-importFrom(Matrix,sparseMatrix)
+importFrom(Matrix,
+  Diagonal,
+  sparseMatrix
+)
 importFrom(data.table,as.data.table)
-importFrom(igraph,V)
-importFrom(igraph,distances)
-importFrom(igraph,subcomponent)
-importFrom(stats,na.omit)
-importFrom(stats,pnorm)
-importFrom(stats,qnorm)
-importFrom(stats,runif)
-importFrom(stats,setNames)
+importFrom(igraph,
+  V,
+  distances,
+  subcomponent
+)
+importFrom(stats,
+  na.omit,
+  pnorm,
+  qnorm,
+  runif,
+  setNames
+)

NEWS.md

@@ -2,6 +2,10 @@
 
 ## Development version
 
+* Added temporal pedigree models. 
+* Added make clean personids for error handling and debugging.
+* Added optional way to reduce file size when the pedigrees share matrices.
+* Preparing for CRAN transition to tidygedcom
 
 ## BGmisc 1.9.0
 * Added `addParentalChain()` and `addParentalFlag()` for tracing parental lineages. These functions support general parental-chain construction and convenient maternal and paternal lineage workflows. `addParentalFlag()` adds a binary indicator for whether each individual belongs to a specified parental chain, which can be useful for filtering, grouping, and lineage-specific summaries.