tess3 doc

bcm-uga · Oct 13, 2016 · d531b88 · d531b88
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diff --git a/R/tess3project.R b/R/tess3project.R
@@ -114,7 +114,7 @@
 #' ## Spatial interpolation of ancestry coefficient
 #' my.colors <- c("tomato", "orange", "lightblue")
 #' my.palette <- CreatePalette(my.colors, 9)
-#' plot(q.matrix, coordinates, method = "map.max",
+#' plot(q.matrix, coordinates, method = "map.max", interpol = kriging(10),
 #'      main = "Ancestry coefficients",
 #'      xlab = "Longitude", ylab = "Latitude",
 #'      resolution = c(500,500), cex = .4,
@@ -130,7 +130,10 @@
 #'     ylab = "-log10(P-values)",
 #'     cex = .3, col = "grey")
 #'
-#' @references \url{http://biorxiv.org/content/early/2016/10/12/080291} \url{https://hal.archives-ouvertes.fr/hal-01222555/}
+#' @references
+#' \url{http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12471/full}
+#' Caye, Kevin et al. (2016) Fast Inference of Individual Admixture Coefficients Using Geographic Data. bioRxiv
+#' doi:10.1101/080291. \url{http://biorxiv.org/content/early/2016/10/12/080291}
 #'
 #' @seealso \code{\link{tess3Main}}, \code{\link{plot.tess3Q}},
 #' \code{\link{barplot.tess3Q}}

diff --git a/Rakefile b/Rakefile
@@ -86,7 +86,7 @@ namespace :pkg do
     end
 
     desc "Deploy the site on gh-pages"
-    task :deploy => [:build, :open] do
+    task :deploy => [:open] do
       puts "== Deploy to gh-pages".green
       colorizedsh "git clone .git gh-pages/"
       Dir.chdir("gh-pages/") do

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -15,6 +15,8 @@ reference:
     - qmatrix
     - pvalue
     - CreatePalette
+    - tess2tess3
+    - plot.tess3
 
 
 navbar:

diff --git a/man/tess3.Rd b/man/tess3.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -15,6 +15,8 @@ reference: @@
         - qmatrix
         - pvalue
         - CreatePalette
+        - tess2tess3
+        - plot.tess3
     navbar:
@@ Expand Down @@