From c2e0507b21273a05d3f87da87b9c74b0815a69e1 Mon Sep 17 00:00:00 2001
From: Malcolm Barrett <malcolmbarrett@gmail.com>
Date: Sun, 24 May 2020 09:35:53 -0700
Subject: [PATCH] fix doi/relative links in docs

---
 README.Rmd                              |  4 ++--
 README.md                               | 11 ++++++-----
 inst/CITATION                           |  4 ++--
 inst/WORDLIST                           |  5 +++++
 vignettes/introduction-to-partition.Rmd |  2 +-
 5 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/README.Rmd b/README.Rmd
index 062dd8e..4d1306f 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -28,7 +28,7 @@ references:
   page: 676-681
   volume: '36'
   issue: '3'
-  URL: 10.1093/bioinformatics/btz661
+  URL: 'https://doi.org/10.1093/bioinformatics/btz661'
 params:
   invalidate_cache: false
 ---
@@ -202,7 +202,7 @@ For more information, see [our paper in Bioinformatics](https://doi.org/10.1093/
 
 ## Contributing 
 
-Please read the [Contributor Guidelines](.github/CODE_OF_CONDUCT.md) prior to submitting a pull request to partition. Also note that this project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
+Please read the [Contributor Guidelines](https://github.com/USCbiostats/partition/blob/master/.github/CONTRIBUTING.md) prior to submitting a pull request to partition. Also note that this project is released with a [Contributor Code of Conduct](https://github.com/USCbiostats/partition/blob/master/.github/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
 
 ## References
 
diff --git a/README.md b/README.md
index 548f911..7b899e0 100644
--- a/README.md
+++ b/README.md
@@ -221,15 +221,16 @@ discusses these issues in more depth (Millstein et al. 2020).
 
 ## Contributing
 
-Please read the [Contributor Guidelines](.github/CODE_OF_CONDUCT.md)
+Please read the [Contributor
+Guidelines](https://github.com/USCbiostats/partition/blob/master/.github/CONTRIBUTING.md)
 prior to submitting a pull request to partition. Also note that this
 project is released with a [Contributor Code of
-Conduct](.github/CODE_OF_CONDUCT.md). By participating in this project
-you agree to abide by its terms.
+Conduct](https://github.com/USCbiostats/partition/blob/master/.github/CODE_OF_CONDUCT.md).
+By participating in this project you agree to abide by its terms.
 
 ## References
 
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
 
 <div id="ref-R-partition">
 
@@ -237,7 +238,7 @@ Millstein, Joshua, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu
 Zhang, Sebastian Stintzing, Volker Heinemann, and Heinz-Josef Lenz.
 2020. “Partition: A Surjective Mapping Approach for Dimensionality
 Reduction.” *Bioinformatics* 36 (3): 676–81.
-[10.1093/bioinformatics/btz661](10.1093/bioinformatics/btz661).
+<https://doi.org/10.1093/bioinformatics/btz661>.
 
 </div>
 
diff --git a/inst/CITATION b/inst/CITATION
index d4b358d..1405b8a 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -9,7 +9,7 @@ citEntry(
   volume   = 36,
   number   = 3,
   pages    = "676–681",
-  url      = "10.1093/bioinformatics/btz661",
+  url      = "https://doi.org/10.1093/bioinformatics/btz661",
   textVersion = "Millstein et al., (2020). Partition: a surjective mapping approach for dimensionality reduction. Bioinformatics, 36(3) 3, 676–681, https://doi.org/10.1093/bioinformatics/btz661"
 )
 
@@ -22,7 +22,7 @@ citEntry(
   volume   = 5,
   number   = 47,
   pages    = "1991",
-  url      = "1991",
+  url      = "https://doi.org/10.21105/joss.01991",
   textVersion = "Barrett et al., (2020). partition: A fast and flexible framework for data reduction in R. Journal of Open Source Software, 5(47), 1991, https://doi.org/10.21105/joss.01991"
 )
 
diff --git a/inst/WORDLIST b/inst/WORDLIST
index dd8a821..0c153e0 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -8,8 +8,11 @@ caae
 Cao
 COC
 colonic
+customizable
 doi
+DOI
 et
+ggcorplot
 ggplot
 ggplots
 Heinemann
@@ -18,6 +21,7 @@ immunochemical
 interpretable
 intraclass
 Intraclass
+joss
 kmeans
 Lenz
 LLoyd
@@ -26,6 +30,7 @@ microbiome
 Microbiome
 microbiomes
 Microbiota
+Millstein
 nrow
 OTU
 OTUs
diff --git a/vignettes/introduction-to-partition.Rmd b/vignettes/introduction-to-partition.Rmd
index d09f946..ac28c42 100644
--- a/vignettes/introduction-to-partition.Rmd
+++ b/vignettes/introduction-to-partition.Rmd
@@ -31,7 +31,7 @@ references:
   page: 676-681
   volume: '36'
   issue: '3'
-  URL: 10.1093/bioinformatics/btz661
+  URL: https://doi.org/10.1093/bioinformatics/btz661
 vignette: >
   %\VignetteIndexEntry{Introduction to Partition}
   %\VignetteEngine{knitr::rmarkdown}