Merge pull request #77 from gaynorr/devel

Devel

.Rbuildignore

@@ -1,11 +1,9 @@
+revdep
+vignettes/web_only/
+docs
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^Notes\.txt$
-^doc$
-^Meta$
-^drafts$
 ^_pkgdown\.yml$
-^docs$
-^pkgdown$
 ^\.github$
-^revdep$
+

.gitignore

@@ -1,14 +1,24 @@
-.Rproj
+*.Rproj
 .Rhistory
+.Rapp.history
 .RData
 .Ruserdata
 config.log
 config.status
+*-Ex.R
+/.*tar.gz
+/*.Rcheck/
 src/*.o
 src/*.so
 src/*.dll
+vignettes/*.html
+vignettes/*.pdf
+.httr-oauth
+*_cache/
+/cache/
+*.utf8.md
+*.knit.md
+.Renviron
 Notes.txt
-Meta
-.Rproj.user
-alphasimr.Rproj
+.Rproj.user/
 docs

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: AlphaSimR
 Type: Package
 Title: Breeding Program Simulations
-Version: 1.2.2
-Date: 2022-7-29
+Version: 1.3.0
+Date: 2022-8-24
 Authors@R: c(person("Chris", "Gaynor", email = "[email protected]",
   role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0558-6656")),
   person("Gregor", "Gorjanc", role = "ctb", 
@@ -28,10 +28,12 @@ Description: The successor to the 'AlphaSim' software for breeding program
   demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
 License: MIT + file LICENSE
 URL: https://github.com/gaynorr/AlphaSimR,
-    https://gaynorr.github.io/AlphaSimR/
+    https://gaynorr.github.io/AlphaSimR/,
+    https://www.edx.org/course/breeding-programme-modelling-with-alphasimr?utm_source=breeding_alphasimr&utm_medium=partner-marketing&utm_campaign=edinburghx
 Encoding: UTF-8
 Depends: R (>= 4.0.0), methods, R6
-Imports: Rcpp (>= 0.12.7)
+Imports: Rcpp (>= 0.12.7), Rdpack
+RdMacros: Rdpack
 LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH
 RoxygenNote: 7.2.1
 Suggests: knitr, rmarkdown, testthat

NAMESPACE

@@ -11,6 +11,7 @@ export(RRBLUP_SCA)
 export(RRBLUP_SCA2)
 export(SimParam)
 export(aa)
+export(addSegSite)
 export(attrition)
 export(bv)
 export(cChr)
@@ -54,6 +55,7 @@ export(mergeGenome)
 export(mergePops)
 export(mutate)
 export(nInd)
+export(newEmptyPop)
 export(newMapPop)
 export(newMegaPop)
 export(newPop)
@@ -86,6 +88,7 @@ export(selectOP)
 export(selectWithinFam)
 export(self)
 export(setEBV)
+export(setMarkerHaplo)
 export(setMisc)
 export(setPheno)
 export(setPhenoGCA)
@@ -129,6 +132,7 @@ exportClasses(TraitAEG)
 exportClasses(TraitAG)
 import(Rcpp)
 importFrom(R6,R6Class)
+importFrom(Rdpack,reprompt)
 importFrom(methods,.hasSlot)
 importFrom(methods,classLabel)
 importFrom(methods,is)