Moved dates functions

tree/algo.go

@@ -1004,65 +1004,3 @@ func CompareWeighted(refTree *Tree, compTrees <-chan Trees, tips, comparetreeide
 
 	return stats, nil
 }
-
-// LTTData describes a Lineage to Time data point
-type LTTData struct {
-	X float64 // Time or Mutations
-	Y int     // Number of lineages
-}
-
-// LTTData describes a Lineage to Time data point
-func (t *Tree) LTT() (lttdata []LTTData) {
-	var lttdatadup []LTTData
-	var dists []float64
-	var err error
-
-	// We compute distance from root to all nodes
-	// If the field [&date=] exists, then takes it
-	// Otherwise, computes the distance to the root
-	if dists, err = t.NodeDates(); err != nil {
-		io.LogWarning(err)
-		io.LogWarning(fmt.Errorf("using mutations instead of dates"))
-		dists = t.NodeRootDistance()
-	}
-
-	// This initializes
-	lttdatadup = make([]LTTData, len(dists))
-	// Version with one point per x, already summed up
-	lttdata = make([]LTTData, len(dists))
-
-	t.PreOrder(func(cur, prev *Node, e *Edge) (keep bool) {
-		lttdatadup[cur.Id()].X = dists[cur.Id()]
-		lttdatadup[cur.Id()].Y = cur.Nneigh()
-		if prev != nil {
-			lttdatadup[cur.Id()].Y -= 2
-		}
-		return true
-	})
-	sort.Slice(lttdatadup, func(i, j int) bool {
-		return lttdatadup[i].X < lttdatadup[j].X
-	})
-
-	lasti := 0
-	for i, l := range lttdatadup {
-		if i == 0 {
-			lttdata[i] = l
-		} else {
-			if lttdata[lasti].X == l.X {
-				lttdata[lasti].Y += l.Y
-			} else {
-				lasti++
-				lttdata[lasti] = l
-			}
-		}
-	}
-	lttdata = lttdata[:lasti+1]
-
-	dists = nil
-	total := 0
-	for i := range lttdata {
-		total += lttdata[i].Y
-		lttdata[i].Y = total
-	}
-	return
-}

tree/dates.go

@@ -0,0 +1,107 @@
+package tree
+
+import (
+	"fmt"
+	"sort"
+
+	"github.com/evolbioinfo/gotree/io"
+)
+
+// LTTData describes a Lineage to Time data point
+type LTTData struct {
+	X float64 // Time or Mutations
+	Y int     // Number of lineages
+}
+
+// LTTData describes a Lineage to Time data point
+func (t *Tree) LTT() (lttdata []LTTData) {
+	var lttdatadup []LTTData
+	var dists []float64
+	var err error
+
+	// We compute distance from root to all nodes
+	// If the field [&date=] exists, then takes it
+	// Otherwise, computes the distance to the root
+	if dists, err = t.NodeDates(); err != nil {
+		io.LogWarning(err)
+		io.LogWarning(fmt.Errorf("using mutations instead of dates"))
+		dists = t.NodeRootDistance()
+	}
+
+	// This initializes
+	lttdatadup = make([]LTTData, len(dists))
+	// Version with one point per x, already summed up
+	lttdata = make([]LTTData, len(dists))
+
+	t.PreOrder(func(cur, prev *Node, e *Edge) (keep bool) {
+		lttdatadup[cur.Id()].X = dists[cur.Id()]
+		lttdatadup[cur.Id()].Y = cur.Nneigh()
+		if prev != nil {
+			lttdatadup[cur.Id()].Y -= 2
+		}
+		return true
+	})
+	sort.Slice(lttdatadup, func(i, j int) bool {
+		return lttdatadup[i].X < lttdatadup[j].X
+	})
+
+	lasti := 0
+	for i, l := range lttdatadup {
+		if i == 0 {
+			lttdata[i] = l
+		} else {
+			if lttdata[lasti].X == l.X {
+				lttdata[lasti].Y += l.Y
+			} else {
+				lasti++
+				lttdata[lasti] = l
+			}
+		}
+	}
+	lttdata = lttdata[:lasti+1]
+
+	dists = nil
+	total := 0
+	for i := range lttdata {
+		total += lttdata[i].Y
+		lttdata[i].Y = total
+	}
+	return
+}
+
+// RTTData describes a Root To Tip Regression
+type RTTData struct {
+	X float64 // Date of the tip
+	Y float64 // Distance to root
+}
+
+// RTTData describes a Root To Tip Regression
+func (t *Tree) RTT() (rttdata []RTTData, err error) {
+	var dists []float64
+	var dates []float64
+
+	// We compute distance from root to all nodes
+	// If the field [&date=] exists, then takes it
+	// Otherwise, computes the distance to the root
+	if dates, err = t.NodeDates(); err != nil {
+		io.LogWarning(err)
+		err = fmt.Errorf("using mutations instead of dates")
+		io.LogWarning(err)
+		return
+	}
+
+	dists = t.NodeRootDistance()
+
+	if len(dists) != len(dates) {
+		err = fmt.Errorf("length of dates differs from length of distances")
+		io.LogWarning(err)
+		return
+	}
+
+	rttdata = make([]RTTData, 0, len(dates))
+	for i, v := range dists {
+		rttdata = append(rttdata, RTTData{dates[i], v})
+	}
+
+	return
+}