diff --git a/README.Rmd b/README.Rmd index cca2494..e37c966 100644 --- a/README.Rmd +++ b/README.Rmd @@ -6,7 +6,7 @@ output: github_document 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. diff --git a/README.md b/README.md index 44da8e2..f00c419 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/inst/CITATION b/inst/CITATION index 6b44bf3..2e0f4f1 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -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" )