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jendelman committed Mar 22, 2023
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2 changes: 1 addition & 1 deletion README.Rmd
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Plant breeders typically use multi-environment datasets that are unbalanced with respect to individuals over time and often within year as well. Experimental designs and the best models for micro-environmental variation may also vary with environment, defined as a location x year combination. These complexities can be handled efficiently with a two-stage analysis, in which best linear unbiased estimates (BLUEs) of genotypic value are computed for each environment in Stage 1 and then used as the response variable in Stage 2. To fully utilize the data, however, the variance-covariance matrix of the estimates from Stage 1 should be included in Stage 2 ([Piepho et al. 2012](https://doi.org/10.1002/bimj.201100219); [Damesa et al. 2017](https://doi.org/10.2134/agronj2016.07.0395)), which is not possible with most software packages for genomics-assisted breeding.

R package StageWise was developed to provide a simple interface for genomic selection and GWAS based on a fully efficient, two-stage analysis. Each phenotypic record is associated with a single genotype id, which is suitable for clonal and inbred lines but not hybrid crops. The ASReml-R package is used for variance component estimation, which requires a license from [VSN International](https://www.vsni.co.uk/software/asreml-r).
R package StageWise was developed to provide a simple interface for genomic selection and GWAS based on a fully efficient, two-stage analysis [(Endelman 2023)](https://doi.org/10.1007/s00122-023-04298-x). Each phenotypic record is associated with a single genotype id, which is suitable for clonal and inbred lines but not hybrid crops. The ASReml-R package is used for variance component estimation, which requires a license from [VSN International](https://www.vsni.co.uk/software/asreml-r).

Software development has been supported by USDA Hatch Project 1013047 and the USDA National Institute of Food and Agriculture (NIFA) Award 2020-51181-32156. The potato datasets were generated with support from NIFA Awards 2016-34141-25707 and 2019-34141-30284, Potatoes USA, the Wisconsin Potato and Vegetable Growers Association, and the University of Wisconsin-Madison.

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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -18,10 +18,11 @@ possible with most software packages for genomics-assisted breeding.

R package StageWise was developed to provide a simple interface for
genomic selection and GWAS based on a fully efficient, two-stage
analysis. Each phenotypic record is associated with a single genotype
id, which is suitable for clonal and inbred lines but not hybrid crops.
The ASReml-R package is used for variance component estimation, which
requires a license from [VSN
analysis [(Endelman 2023)](https://doi.org/10.1007/s00122-023-04298-x).
Each phenotypic record is associated with a single genotype id, which is
suitable for clonal and inbred lines but not hybrid crops. The ASReml-R
package is used for variance component estimation, which requires a
license from [VSN
International](https://www.vsni.co.uk/software/asreml-r).

Software development has been supported by USDA Hatch Project 1013047
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9 changes: 5 additions & 4 deletions inst/CITATION
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Expand Up @@ -3,8 +3,9 @@ citHeader("To cite the StageWise package in publications, please use")
citEntry(entry="Article",
title="Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection",
author=personList(as.person("J. B. Endelman")),
year=2022,
journal="bioRxiv",
pages="BIORXIV/2022/509884",
textVersion="Endelman JB (2022) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection. BIORXIV/2022/509884"
year=2023,
journal="Theoretical and Applied Genetics",
volume="136",
pages="65",
textVersion="Endelman JB (2023) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection. Theoretical and Applied Genetics 136:65"
)

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