add doc & fix warnings

.gitignore

@@ -32,5 +32,7 @@ vignettes/*.pdf
 *.utf8.md
 *.knit.md
 
+*.o
+*.so
 
 .Rproj.user

R/simulation.R

@@ -15,6 +15,9 @@
 #' @param na integer :
 #' @param natba integer : Min nb of genotype copies to consider this genotype as advantageous
 #' @param nbreps integer :
+#' @param have_rescuers logical : if you want rescuers file
+#' @param have_rate logical : if you want rate file (you need have_rescuers=TRUE)
+#' @param output_path string : the output path
 #' @param verbose logical : if you want a verbose program
 #' @return array :
 simulation <- function(max_geno = 500, range = c(-0.05, -0.1, -0.15),
@@ -146,7 +149,7 @@ Rbuiltlandscape <- function(n, ne, Es, so, na)
   xo <- numeric(n)
   if (so != 0) { #if so = 0, all the genotypic values stay at 0
     x1 <- rnorm(n)
-    xo <- x1 * sqrt(2 * so / (t(x1) %*% S %*% x1) )
+    xo <- x1 * as.vector(sqrt(2 * so / (t(x1) %*% S %*% x1) ))
   }
 
   return(list(M=M, Sb=S, A=A, xo=xo))