Merge pull request gaynorr#267 from gregorgorjanc/gregorgorjanc/issue193

Add link to the on-line course in pkgdown

Author: gaynorr

README.md

@@ -1,15 +1,24 @@
 # README #
 
-[![R-CMD-check](https://github.com/gaynorr/AlphaSimR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/gaynorr/AlphaSimR/actions/workflows/R-CMD-check.yaml)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/AlphaSimR)](https://cran.r-project.org/package=AlphaSimR)
+CRAN stats: [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/AlphaSimR)](https://cran.r-project.org/package=AlphaSimR)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/AlphaSimR)](https://cran.r-project.org/package=AlphaSimR)
 [![](http://cranlogs.r-pkg.org/badges/AlphaSimR)](https://cran.r-project.org/package=AlphaSimR)
 
+R CMD checks: [![CRAN](https://cranchecks.info/badges/summary/AlphaSimR?label=CRAN)](https://cran.r-project.org/web/checks/check_results_AlphaSimR.html)
+[![R universe](https://gaynorr.r-universe.dev/AlphaSimR/badges/checks?label=R-universe)](https://gaynorr.r-universe.dev/AlphaSimR)
+[![GitHub](https://img.shields.io/github/actions/workflow/status/gaynorr/AlphaSimR/R-CMD-check.yaml?label=GitHub)](https://github.com/gaynorr/AlphaSimR/actions/workflows/R-CMD-check.yaml)
+
 The successor to the 'AlphaSim' software for breeding program simulation (Faux et al., 2016; https://doi.org/10.3835/plantgenome2016.02.0013). Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history (Chen et al., 2009; https://doi.org/10.1101/gr.083634.108).
 
-## Publication
+## Publications
+
+Gaynor, R Chris and Gorjanc, Gregor and Hickey, John M (2021) AlphaSimR: an R package for breeding program simulations. G3 Gene|Genomes|Genetics, 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.
+
+Bančič, Jon and Greenspoon, Philip and Gaynor, R Chris and Gorjanc, Gregor (2024) Plant breeding simulations with AlphaSimR. Crop Science, 65(1):e21312. https://doi.org/10.1002/csc2.21312.
 
-Gaynor, R. Chris, Gregor Gorjanc, and John M. Hickey. 2021. AlphaSimR: an R package for breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.
+## Online course
+
+Free course on breeding program simulations and how to use AlphaSimR is available on [edX](https://www.edx.org/learn/animal-breeding/the-university-of-edinburgh-breeding-programme-modelling-with-alphasimr).
 
 ## Download
 
@@ -28,4 +37,3 @@ To install use:
 To install with vignettes use:
 
     devtools::install_github(repo="gaynorr/AlphaSimR@devel", build_vignettes=TRUE)
-

inst/CITATION

@@ -1,22 +1,25 @@
 bibentry(
-  bibtype  = "Article",
-  title    = "AlphaSimR: an R package for breeding program simulations",
-  author   = "R Chris Gaynor, Gregor Gorjanc, John M Hickey",
-  journal  = "G3 Gene|Genomes|Genetics",
-  year     = "2021",
-  volume   = "11",
-  number   = "jkaa07",
-  issue    = "2",
-  url      = "https://doi.org/10.1093/g3journal/jkaa017"
+  bibtype = "Article",
+  title   = "AlphaSimR: an R package for breeding program simulations",
+  author  = "Gaynor, R Chris and Gorjanc, Gregor and Hickey, John M",
+  journal = "G3 Gene|Genomes|Genetics",
+  year    = "2021",
+  volume  = "11",
+  number  = "2",
+  pages   = "jkaa07",
+  doi     = "10.1093/g3journal/jkaa017",
+  url     = "https://doi.org/10.1093/g3journal/jkaa017"
 )
 
 bibentry(
-  bibtype  = "Article",
-  title    = "Plant breeding simulations with AlphaSimR",
-  author   = "Jon Bančič, Philip Greenspoon, R Chris Gaynor, Gregor Gorjanc",
-  journal  = "Crop Science",
-  year     = "2025",
-  volume   = "65",
-  number   = "e21312",
-  url      = "https://doi.org/10.1002/csc2.21312"
+  bibtype = "Article",
+  title   = "Plant breeding simulations with AlphaSimR",
+  author  = "Bančič, Jon and Greenspoon, Philip and Gaynor, R Chris and Gorjanc, Gregor",
+  journal = "Crop Science",
+  year    = "2024",
+  volume  = "65",
+  number  = "1",
+  pages   = "e21312",
+  doi     = "10.1002/csc2.21312",
+  url     = "https://doi.org/10.1002/csc2.21312"
 )