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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
1fb19d0
finalzied refactoring according to CRAN standards
May 20, 2026
65d48fd
Updated functions and descriptions to be CRAN compliant and updatede …
May 21, 2026
9b16038
updated parentage functions to standardize inputs and outputs
May 26, 2026
26bae5f
updated functions to work as a workflow accepting inputs from objects…
May 26, 2026
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2 changes: 2 additions & 0 deletions .Rbuildignore
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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
20 changes: 18 additions & 2 deletions 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)
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josuechinchilla marked this conversation as resolved.
Expand All @@ -40,21 +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)
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josuechinchilla marked this conversation as resolved.
Comment on lines +66 to +72
importFrom(janitor,clean_names)
importFrom(pwalign,nucleotideSubstitutionMatrix)
importFrom(pwalign,pairwiseAlignment)
importFrom(readr,read_csv)
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