Merge pull request #23 from huizezhang-sherry/master

add stringy calculated based on diameter and length in Wilkinson 2005

Author: harriet-mason

NAMESPACE

@@ -36,6 +36,9 @@ S3method(sc_striated2,scree)
 S3method(sc_stringy,default)
 S3method(sc_stringy,igraph)
 S3method(sc_stringy,scree)
+S3method(sc_stringy2,default)
+S3method(sc_stringy2,igraph)
+S3method(sc_stringy2,scree)
 export(calc_scags)
 export(calc_scags_wide)
 export(draw_alphahull)
@@ -56,6 +59,7 @@ export(sc_splines)
 export(sc_striated)
 export(sc_striated2)
 export(sc_stringy)
+export(sc_stringy2)
 export(sc_striped)
 export(scree)
 export(top_pairs)

R/mst.R

@@ -45,6 +45,34 @@ sc_stringy.igraph <- function(x, y=NULL) {
   sum(vertex_counts == 2) / (length(vertex_counts) - sum(vertex_counts == 1))
 }
 
+#' @rdname sc_stringy
+#' @export
+sc_stringy2 <- function(x, y) UseMethod("sc_stringy2")
+
+#' @rdname sc_stringy
+#' @export
+sc_stringy2.default <- function(x, y){
+  #input: x and y are vectors
+  sc <- scree(x, y)
+  sc_stringy2.scree(sc)
+}
+
+#' @rdname sc_stringy
+#' @export
+sc_stringy2.scree <- function(x, y=NULL) {
+  #input: x is a scree, no y
+  mst <- gen_mst(x$del, x$weights)
+  sc_stringy2.igraph(mst)
+}
+
+#' @rdname sc_stringy
+#' @export
+sc_stringy2.igraph <- function(x, y=NULL) {
+  #input: x is the MST igraph object
+  diameter <- igraph::get_diameter(x)
+  length(diameter) / (length(x) - 1)
+}
+
 #' Compute striated scagnostic measure using MST
 #'
 #' @param x numeric vector of x values

man/sc_stringy.Rd

@@ -26,6 +26,7 @@ y1 <- c(0,10,20,30,40,50,60,70,80,90,100, 25)
 
 test_that("Stringy Scagnotist", {
   expect_equal(sc_stringy(x1,y1), (8/9))
+  expect_equal(sc_stringy2(x1,y1), 1)
 })
 
 #Striated test