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Added parentage functions #59

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f590dad
Merge pull request #58 from Breeding-Insight/development
josuechinchilla Apr 22, 2026
20d2764
corrected importFrom statement in parentage functions and ped_check
Apr 22, 2026
f2d3f40
updated NAMESPACE to reflect updated importFrom statements
Apr 22, 2026
c1fe543
Update R/check_ped.R
josuechinchilla Apr 22, 2026
0a13483
updated error handling and reporting for check_ped, Also major improv…
Apr 24, 2026
9bbc507
updated error handling and reporting for check_ped
Apr 24, 2026
f798362
updated parentage functions to work allow user to display NA or not, …
Apr 27, 2026
03725d8
Made edits suggested by autopilot
Apr 27, 2026
506a47f
added edits suggested by copilot
Apr 27, 2026
977e070
modified default params
Apr 28, 2026
5db5fa2
Added authors fror functions and made headers concise
Apr 28, 2026
6b84e18
staged comments for next push
May 20, 2026
4eb79bb
removed zip option and added specific correction arguments
May 20, 2026
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2 changes: 2 additions & 0 deletions .Rbuildignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,5 @@
^package-code\.Rmd$
^docs$
^CRAN-SUBMISSION$
^\.positai$
^\.claude$
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -4,3 +4,4 @@
.Ruserdata
revdep/
.DS_Store
.positai
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -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:
Expand Down Expand Up @@ -74,3 +73,4 @@ Suggests:
polyRAD,
testthat (>= 3.0.0)
RdMacros: Rdpack
Config/roxygen2/version: 8.0.0
18 changes: 17 additions & 1 deletion NAMESPACE
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Expand Up @@ -23,8 +23,8 @@ export(merge_MADCs)
export(solve_composition_poly)
export(thinSNP)
export(updog2vcf)
export(validate_pedigree)
import(dplyr)
import(janitor)
import(parallel)
import(quadprog)
import(stringr)
Comment on lines 25 to 30
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Copilot AI Apr 27, 2026

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janitor was removed from the NAMESPACE imports, and there are no remaining references in the R code. The package still lists janitor under Imports in DESCRIPTION, which will keep it as a hard dependency unnecessarily. Consider removing it from DESCRIPTION (or re-adding the NAMESPACE import if it's still intended to be required).

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Expand All @@ -46,15 +46,29 @@ 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,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)
Comment on lines +65 to +71
importFrom(pwalign,nucleotideSubstitutionMatrix)
importFrom(pwalign,pairwiseAlignment)
importFrom(readr,read_csv)
Expand All @@ -65,12 +79,14 @@ importFrom(stats,cor)
importFrom(stats,reorder)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(tools,file_path_sans_ext)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(utils,zip)
importFrom(vcfR,extract.gt)
importFrom(vcfR,maf)
importFrom(vcfR,read.vcfR)
Expand Down
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