From 8d96ef235d4a53030224e5a4748bb8256771df99 Mon Sep 17 00:00:00 2001
From: YanHanChen <42162906+YanHanChen@users.noreply.github.com>
Date: Mon, 16 Mar 2020 20:34:47 +0800
Subject: [PATCH 1/4] Fix the bootstrap tips label problem

Fix a problem in bootstrap in which the tips label doesn't match to correct tips abundances, leading to incorrect accumulation of inter nodes.
---
 R/iNextPD.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/iNextPD.R b/R/iNextPD.R
index dde0e03..29b07fa 100644
--- a/R/iNextPD.R
+++ b/R/iNextPD.R
@@ -36,7 +36,7 @@ iNextPD.Ind <- function(x, labels, phy, q, size=NULL, endpoint=2*sum(x), knots=4
   U <- tmp$branch_abun
   L <- tmp$branch_length
   names(x) <- labels
-  x <- x[names(phy$leaves)]
+  # x <- x[names(phy$leaves)]
   phd.hat <- PhD.m(n, x, U, L, q, m)
   C.hat <- Coverage_(x, "abundance", m)
   

From a2b7dbae26be81165125f1fb0aad966553431c11 Mon Sep 17 00:00:00 2001
From: YanHanChen <42162906+YanHanChen@users.noreply.github.com>
Date: Mon, 16 Mar 2020 20:50:50 +0800
Subject: [PATCH 2/4] fix the incidence part of previous problem

---
 R/iNextPD.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/iNextPD.R b/R/iNextPD.R
index 29b07fa..a5cc679 100644
--- a/R/iNextPD.R
+++ b/R/iNextPD.R
@@ -111,7 +111,7 @@ iNextPD.Sam <- function(x, labels, phy, q, size=NULL, endpoint=2*ncol(x), knots=
   L <- tmp$branch_length
   xx <- rowSums(x)
   names(xx) <- labels
-  xx <- xx[names(phy$leaves)]
+  # xx <- xx[names(phy$leaves)]
   phd.hat <- PhD.m(nT, xx, U, L, q, t)
   C.hat <- Coverage_(Spec, "incidence",t)
   

From 43bcad3e34ca7098ebaf1ed51825136683eb5a7c Mon Sep 17 00:00:00 2001
From: YanHanChen <42162906+YanHanChen@users.noreply.github.com>
Date: Mon, 16 Mar 2020 21:16:02 +0800
Subject: [PATCH 3/4] Update NEWS

---
 NEWS | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS b/NEWS
index b94e5a8..f8bd111 100644
--- a/NEWS
+++ b/NEWS
@@ -7,3 +7,7 @@ iNextPD 0.3.1
 ----------------------------------------------------------------
 - Import `girdExtra`, `ggthemes` to pass R check
 - Do not run a example in `estimatePD`
+
+iNextPD 0.3.2
+----------------------------------------------------------------
+- Fix the bootstrap tips label problem

From d889361d7152ea27ac620db15651d5d51501c8ea Mon Sep 17 00:00:00 2001
From: YanHanChen <42162906+YanHanChen@users.noreply.github.com>
Date: Mon, 16 Mar 2020 21:16:21 +0800
Subject: [PATCH 4/4] Update DESCRIPTION

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 27d3b8a..2afdd25 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: iNextPD
 Type: Package
 Title: Interpolation and Extrapolation for Phylogenetic Diversity
-Version: 0.3.1
+Version: 0.3.2
 Date: 2016-11-10
 Authors@R: c(person("T. C.", "Hsieh", role = c("aut", "cre", "cph"), email =
     "euler96@gmail.com"),  person("Chun-Huo", "Chiu", role = "ths", email =