Package: PopVar 1.3.1
Jeffrey Neyhart
PopVar: Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation
The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015, <doi:10.2135/cropsci2015.01.0030>). A dataset 'think_barley.rda' is included for reference and examples.
Authors:
PopVar_1.3.1.tar.gz
PopVar_1.3.1.zip(r-4.5)PopVar_1.3.1.zip(r-4.4)PopVar_1.3.1.zip(r-4.3)
PopVar_1.3.1.tgz(r-4.4-any)PopVar_1.3.1.tgz(r-4.3-any)
PopVar_1.3.1.tar.gz(r-4.5-noble)PopVar_1.3.1.tar.gz(r-4.4-noble)
PopVar_1.3.1.tgz(r-4.4-emscripten)PopVar_1.3.1.tgz(r-4.3-emscripten)
PopVar.pdf |PopVar.html✨
PopVar/json (API)
NEWS
| # Install 'PopVar' in R: |
| install.packages('PopVar', repos = c('https://cranhaven.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cranhaven/cranhaven.r-universe.dev/issues
- G.in_ex - An example barley dataset
- G.in_ex_imputed - An example barley dataset
- G.in_ex_mat - An example barley dataset
- cross.tab_ex - An example barley dataset
- map.in_ex - An example barley dataset
- y.in_ex - An example barley dataset
Last updated 12 days agofrom:e905ffdaab (on package/PopVar). Checks:OK: 5 NOTE: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 05 2024 |
| R-4.5-win | NOTE | Sep 05 2024 |
| R-4.5-linux | NOTE | Sep 05 2024 |
| R-4.4-win | OK | Sep 05 2024 |
| R-4.4-mac | OK | Sep 05 2024 |
| R-4.3-win | OK | Sep 05 2024 |
| R-4.3-mac | OK | Sep 05 2024 |
Exports:mppop_predict2mppop.predictpop_predict2pop.predictpop.predict2x.val
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genomic breeding tools to 1) predict standard statistics and correlated response in plant populations, and 2) performs cross-validation to estimate genome-wide prediction accuracy | PopVar-package PopVar |
| Internal functions | calc_marker_effects internal maf_filt par_name par_position tails XValidate_Ind XValidate_nonInd |
| Predict genetic variance and genetic correlations in multi-parent populations using a deterministic equation. | mppop.predict mppop_predict2 |
| A genome-wide procedure for predicting genetic variance and correlated response in bi-parental breeding populations | pop.predict |
| Predict genetic variance and genetic correlations in bi-parental populations using a deterministic model | pop.predict2 pop_predict2 |
| An example barley dataset | cross.tab_ex G.in_ex G.in_ex_imputed G.in_ex_mat map.in_ex think_barley.rda y.in_ex |
| Estimate genome-wide prediction accuracy using cross-validation | x.val |
