Add parentage functions

.Rbuildignore

@@ -10,3 +10,5 @@
 ^package-code\.Rmd$
 ^docs$
 ^CRAN-SUBMISSION$
+^\.positai$
+^\.claude$

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 revdep/
 .DS_Store
+.positai

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BIGr
 Title: Breeding Insight Genomics Functions for Polyploid and Diploid Species
-Version: 0.7.2
+Version: 0.8.0
 Authors@R: c(person(given='Alexander M.',
                     family='Sandercock',
                     email='sandercock.alex@gmail.com',
@@ -44,7 +44,6 @@ URL: https://github.com/Breeding-Insight/BIGr
 BugReports: https://github.com/Breeding-Insight/BIGr/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Depends: R (>= 4.4.0)
 biocViews:
 Imports: 
@@ -74,3 +73,4 @@ Suggests:
     polyRAD,
     testthat (>= 3.0.0)   
 RdMacros: Rdpack
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -25,7 +25,6 @@ export(thinSNP)
 export(updog2vcf)
 export(validate_pedigree)
 import(dplyr)
-import(janitor)
 import(parallel)
 import(quadprog)
 import(stringr)
@@ -41,21 +40,37 @@ importFrom(data.table,as.data.table)
 importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,fread)
-importFrom(data.table,fwrite)
+importFrom(data.table,is.data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,set)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
+importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
+importFrom(dplyr,first)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_modify)
+importFrom(dplyr,if_else)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
+importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
+importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,where)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_minimal)
+importFrom(janitor,clean_names)
 importFrom(pwalign,nucleotideSubstitutionMatrix)
 importFrom(pwalign,pairwiseAlignment)
 importFrom(readr,read_csv)