Familia 2.2.0

• Every tab has an Example files link in its Inputs box that downloads a small simulated data set (inst/extdata, made by data-raw/make_example_data.R). It is the data set used in the user guide.
• Find Parentage: new optional Founders File, shown for Fill in pedigree and passed to the BIGpopA founders_file argument. Founders with both parents unknown are skipped; without the file a notification warns that every individual with both parents unknown, founders included, gets a full parent search.
• PolyBreedTools: the Results Table and the Excel file include R2, the model fit of each sample, explained in the Instructions and Help. The Instructions no longer say that the first column must be ID (any column named ID, in any case, is used). The Example Inputs box shows and downloads the example files.
• Validate Pedigree: the founders file also accepts .csv and .tsv, and the Instructions explain what it does.
• Help: the Best male / female parent panels showed <code> tags as text; the method panels now give the score each method uses.
• SNMF: VCF uploads are read with the same reader as the other tabs (BIGpopA vcf_to_dosage(), which drops multiallelic markers) and written as a LEA .geno file directly. Polyploid VCFs used to fail with “‘R’ matrix can only contains 0, 1, 2 or 9”, because LEA::write.geno() only accepts diploid calls; ploidy up to 8 is now supported.
• Check for Updates looked up the BIGapp releases and compared versions as text. It now checks the Familia releases, compares version numbers (so 2.10.0 is newer than 2.9.0) and shows a message when GitHub cannot be reached.
• The logo in the top bar was not shown on case-sensitive file systems (e.g. Linux servers).
• Validate Pedigree and Find Parentage no longer write Rplots.pdf to the working directory (or open a plot window) when they run; the plot is only shown in the app.
• Removed unused internal code and imports.
• New short vignette (vignette("Familia")) that explains how to launch the app and what each tab does.
• Find Parentage: the progeny input is now labeled Progeny / Pedigree File and its instructions state that a pedigree file is accepted.
• Find Parentage: new Top N input reports the best N candidates per progeny, and results include a tied_candidates count that flags ambiguous assignments.
• Find Parentage: new Fill in pedigree method fills missing parents of a pedigree. It is grayed out unless the progeny file is a 3-column pedigree (id, male_parent, female_parent); the parents file with sex M/F/A is still required.
• Validate Pedigree: new Marker Summary table (per-marker trios tested, mismatches and mismatch %) and marker_summary.txt in the download.
• Validate Pedigree: new Marker Trio Table (status of every marker in every trio, from BIGpopA marker_trio_table) shown in the results and saved as marker_trio_table.txt in the download.
• Validate Pedigree no longer reports suggested replacement parents (removed in BIGpopA 2.2.0); use Find Parentage > Fill in pedigree on the corrected pedigree instead.
• Updated the Help panels for the new options.
• Requires ‘BIGpopA’ (>= 2.2.0).

Familia 2.1.0

• Find Parentage, Validate Pedigree and PolyBreedTools now accept genotypes as text files (.txt/.csv), VCF files (.vcf/.vcf.gz), or ‘PLINK’ .ped files, in addition to the previous tab-separated format. VCF calls are converted to allele-B dosages using the selected Ploidy; .ped files are diploid only.
• PolyBreedTools: a .map upload appears for each .ped genotype file so markers are matched by name. If either genotype file is a .ped, both must be; the validation .ped is coded with the reference panel’s counted allele per marker.
• PolyBreedTools: new Assignment threshold (%) input. Samples whose highest line proportion is below the threshold are labeled “Undetermined”. Changes apply without re-running the estimation. The default is 50; use 0 to always assign the highest line.
• SNMF: the plot, Q matrix and downloads use the best (lowest cross-entropy) run for the selected K by default. The manual run selector moved to an Advanced Options dialog for diagnostics; changing K or re-running resets to the best run. The Help panel now explains run selection.
• Updated the in-app Instructions and Help panels for the new input formats.
• Column names id, male_parent, female_parent and sex in uploaded files are no longer case sensitive (e.g. ID, Male_Parent are accepted).
• VCF uploads (all modules, including SNMF) now stop with a clear message when the selected Ploidy differs from the most common ploidy in the file, and suggest the ploidy to use (e.g. “The VCF looks tetraploid (ploidy 4) … Set Ploidy to 4 and run again.”).
• Fixed “Save Image” downloads: the file type is set explicitly, svg export works without the ‘svglite’ package, and saving errors are shown in the app.
• Requires ‘BIGpopA’ (>= 2.1.0).

Familia 2.0.0

• Added a Ploidy selector to the Find Parentage and Validate Pedigree tabs, passed through to ‘BIGpopA’ so pedigree validation and parentage assignment now support any ploidy. Even ploidy uses the full polysomic Mendelian test; odd ploidy (e.g. triploid) uses a homozygosity-based check. Default is 2 (diploid).
• Updated the in-app Instructions and Help panels to document the Ploidy option and to generalize genotype dosage coding to 0, 1, …, ploidy.
• Requires ‘BIGpopA’ (>= 2.0.0).

Familia 1.0.4

• Updated the funding attribution banner on the Home tab to read “University of Florida” instead of “Cornell University”, reflecting the correct institution.
• Added URL and BugReports fields to DESCRIPTION.

Familia 1.0.3

• Addressed CRAN reviewer feedback: removed the redundant “R” from the Title; wrapped software names (‘shiny’, ‘LEA’) in single quotes in the Title and Description; added method references to the Description (sNMF, the ‘LEA’ package, the breed-composition methods of Funkhouser et al. and Sandercock et al., and the ‘BIGpopA’ package) with DOIs or canonical URLs; and replaced the \dontrun{} example wrapper in run_app() with if(interactive()){}.

Familia 1.0.2

*Fixed test directory for CRAN submission

Familia 1.0.1

• Prepared app for CRAN submission.
• Replaced the tidyverse meta-package dependency with dplyr and tidyr.
• Declared ggplot2, curl, and httr in Imports and removed the unused viridis dependency.
• Removed the Remotes field now that BIGpopA is available on CRAN.

Familia 0.1.0

• Initial Golem framework