Issue rqtl#142: let calc_sdp() take a vector

NEWS.md

@@ -24,6 +24,8 @@
 - Make the [vdiffr](https://vdiffr.r-lib.org) package optional: only
   test the plots locally, and only if vdiffr is installed.
 
+- `calc_sdp()` can now take a plain vector (Issue #142).
+
 ### Bug fixes
 
 - Fixed [Issue #181](https://github.com/rqtl/qtl2/issues/181), where

R/calc_sdp.R

@@ -23,9 +23,14 @@ calc_sdp <-
     function(geno)
 {
     # tolerate data frames, but convert to matrix
-    if(!is.matrix(geno) && is.data.frame(geno))
-        geno <- as.matrix(geno)
-    if(!is.matrix(geno)) stop("geno should be a matrix")
+    if(!is.matrix(geno)) {
+        if(is.data.frame(geno)) {
+            geno <- as.matrix(geno)
+        } else {
+            geno <- rbind(geno)
+            dimnames(geno) <- NULL
+        }
+    }
 
     n_str <- ncol(geno)
 

tests/testthat/test-calc_sdp.R

@@ -42,6 +42,10 @@ test_that("calc_sdp works", {
     g <- g[n_AA > 0 & n_AA < 8,]
     expect_equal(calc_sdp(g),
                  apply(g, 1, function(a) sum(((a-1)/2)*2^(seq(along=a)-1))))
+
+    expect_equal( calc_sdp( c(1,1,1,3,1,1,1,1) ), 8)
+    expect_equal( calc_sdp( data.frame(1,1,1,3,1,1,1,1)),  8)
+
 })