From 90486be6c92d35ebbf6813762c0266ad01783780 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 3 Jan 2022 20:09:37 +0000
Subject: [PATCH] Update citations

---
 DESCRIPTION                      | 7 ++++---
 R/tree_distance_kendall-colijn.R | 2 +-
 README.md                        | 7 ++++---
 inst/CITATION                    | 8 ++++----
 inst/REFERENCES.bib              | 6 ++++--
 5 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 27d6db75..7f1adfc5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,9 +27,10 @@ Description: Implements measures of tree similarity, including
   the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
   Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. 
   (1996) <doi:10.1007/3-540-61332-3_168>.
-  Includes tools for visualizing mappings of tree space (Smith 2022), for
-  calculating the median of sets of trees, and for computing the information
-  content of trees and splits.
+  Includes tools for visualizing mappings of tree space (Smith 2022)
+  <doi:10.1093/sysbio/syab100>,
+  for calculating the median of sets of trees,
+  and for computing the information content of trees and splits.
 Copyright: Incorporates Jonker-Volgenant Linear Assignment Problem 
   implementation by Roy Jonker, modified by Yong Yang after Yi Cao.
 URL: https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist/
diff --git a/R/tree_distance_kendall-colijn.R b/R/tree_distance_kendall-colijn.R
index 15803953..47bce10c 100644
--- a/R/tree_distance_kendall-colijn.R
+++ b/R/tree_distance_kendall-colijn.R
@@ -26,7 +26,7 @@
 #' `PathVector` returns the number of edges between each pair of leaves (per
 #' Steel & Penny 1993).
 #' `SplitVector` returns the size of the smallest split that contains each
-#' pair of leaves (per Smith, forthcoming).
+#' pair of leaves (per Smith, 2022).
 #' 
 #' @templateVar returns `KendallColijn()` returns
 #' @template distReturn
diff --git a/README.md b/README.md
index 8305b8c3..b7bbdfee 100644
--- a/README.md
+++ b/README.md
@@ -98,7 +98,7 @@ devtools::install_github('ms609/TreeDist')
 # Tree space analysis
 
 Construct tree spaces and readily visualize projected landscapes, avoiding
-common analytical pitfalls (Smith, forthcoming),
+common analytical pitfalls (Smith, 2022),
 using the inbuilt graphical user interface:
 
 ```r
@@ -168,8 +168,9 @@ metrics for comparing phylogenetic
 trees](https://dx.doi.org/10.1093/bioinformatics/btaa614).
 _Bioinformatics_, 36, 5007–5013.
 
-- Smith, M.R. (2022)
-Robust analysis of phylogenetic tree space. _Systematic Biology_, in press.
+- Smith, M.R. (2022) [Robust analysis of phylogenetic tree
+space](https://dx.doi.org/10.1093/sysbio/syab100).
+_Systematic Biology_, syab100.
 
 
 Please note that the 'TreeDist' project is released with a
diff --git a/inst/CITATION b/inst/CITATION
index 86c8f6b6..bef54c3a 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -30,21 +30,21 @@ for comparing phylogenetic trees. ",
              
 citEntry(entry = "article",
       key = "Smith2022",
-      doi = "10.1093/sysbio/syXXXXX",
+      doi = "10.1093/sysbio/syab100",
       title = "Robust analysis of phylogenetic tree space",
       author = personList(as.person("Martin R. Smith")),
       journal = "Systematic Biology",
       volume = "",
       number = "",
-      pages = "in press",
+      pages = "syab100",
       year = "2022",
 
       textVersion =
       paste0("Smith, M.R. (2022).",
              " Robust analysis of phylogenetic tree space. ", 
              " Systematic Biology",
-             " in press.",
-             " doi: 10.1093/sysbio/syXXXXX"))
+             " syab100.",
+             " doi: 10.1093/sysbio/syab100"))
 
 citEntry(entry = "manual",
       key = "TreeDist",
diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib
index 992f253d..543b9b82 100644
--- a/inst/REFERENCES.bib
+++ b/inst/REFERENCES.bib
@@ -399,7 +399,8 @@ @article{SmithCons
   author = {Smith, Martin R.},
   title = {Using information theory to detect rogue taxa and improve consensus trees},
   journal = {Systematic Biology},
-  pages = {forthcoming},
+  pages = {syab099},
+  doi = {10.1093/sysbio/syab099},
   year = {2022}
 }
 
@@ -418,7 +419,8 @@ @article{SmithSpace
   author = {Smith, Martin R.},
   title = {Robust analysis of phylogenetic tree space},
   journal = {Systematic Biology},
-  pages = {in production},
+  pages = {syab100},
+  doi = {10.1093/sysbio/syab100},
   year = {2022}
 }