NEWS
Familia 2.2.0 (2026-10-28)
- 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 (2026-08-24)
- 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 (2026-07-29)
- 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