diff --git a/cran-comments.md b/cran-comments.md index 154666bd..b0cbd3f9 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,7 +2,7 @@ * local OS X install, R 3.3.0 * ubuntu 12.04 (on travis-ci), devel [2016-06-08 r70732] and R 3.3.0 -* win-builder (devel [2016-06-06 r70718] and release [3.2.4]) +* win-builder (devel [2016-06-08 r70728]) ## R CMD check results @@ -19,34 +19,6 @@ Found the following (possibly) invalid URLs: Message: Unauthorized ``` -### WARNING on win-builder devel: - -``` -* checking re-building of vignette outputs ... WARNING -Error in re-building vignettes: - ... -Loading required package: adegenet -Loading required package: ade4 - - /// adegenet 2.0.1 is loaded //////////// - - > overview: '?adegenet' - > tutorials/doc/questions: 'adegenetWeb()' - > bug reports/feature requests: adegenetIssues() - - -This is poppr version 2.1.1.99.67. To get started, type package?poppr -OMP parallel support: available - -This version of poppr is under development. -If you find any bugs, please report them at https://github.com/grunwaldlab/poppr/issues -Loading required package: ape -Quitting from lines 287-295 (mlg.Rmd) -Error: processing vignette 'mlg.Rmd' failed with diagnostics: -invalid gray level, must be in [0,1]. -Execution halted -``` - This is indeed a valid URL ## Downstream dependencies diff --git a/vignettes/mlg.Rmd b/vignettes/mlg.Rmd index 9dbb819f..9b0a9f16 100644 --- a/vignettes/mlg.Rmd +++ b/vignettes/mlg.Rmd @@ -278,25 +278,6 @@ Notice that all the MLGs are the same as the originally defined MLGs. Using a threshold of zero allows two MLGs separated by zero genetic distance to remain mutually unique. -### Minimum spanning networks - -Now we have all of our MLLs collapsed together, but perhaps a better way to -visualize it would be to use `poppr.msn()`: - -```{r} -# Threshold of 1 -set.seed(9001) -g1 <- poppr.msn(x, xdis, threshold = 1, include.ties = TRUE, - vertex.label.color = "firebrick", vertex.label.font = 2) -# Threshold of 1 + e -set.seed(9001) -g2 <- poppr.msn(x, xdis, threshold = 1 + e, include.ties = TRUE, - vertex.label.color = "firebrick", vertex.label.font = 2) -``` - -Notice how the genotypes collapse into a single node. Both `poppr.msn()` and -`bruvo.msn()` will calculate and plot these minimum spanning networks. - ### Setting the genotypes As demonstrated at the beginning of this section, if we wanted to reassign our