From e60a697ad43910e19102aab6e192da04134d7ea0 Mon Sep 17 00:00:00 2001 From: adamhsparks Date: Thu, 16 May 2024 03:57:40 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20openplan?= =?UTF-8?q?tpathology/hagis@da2ecb60d2648f2c9b161a21e18f0f859da83949=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- LICENSE-text.html | 2 +- LICENSE.html | 2 +- articles/betadiversity.html | 2 +- articles/hagis.html | 2 +- articles/index.html | 2 +- authors.html | 6 +++--- index.html | 5 ++--- news/index.html | 9 +++++++-- pkgdown.yml | 2 +- reference/P_sojae_survey.html | 2 +- reference/autoplot.hagis.complexities.html | 2 +- reference/autoplot.hagis.gene.summary.html | 2 +- reference/calculate_complexities.html | 5 ++--- reference/calculate_diversities.html | 7 +++++-- reference/create_binary_matrix.html | 5 ++--- reference/diversities_table.html | 2 +- reference/hagis-package.html | 2 +- reference/index.html | 2 +- reference/individual_pathotypes.html | 2 +- reference/reexports.html | 2 +- reference/sample_meta.html | 2 +- reference/summarize_gene.html | 6 ++---- 25 files changed, 41 insertions(+), 38 deletions(-) diff --git a/404.html b/404.html index 8f9f138..2e4250c 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index e385468..84b93bf 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 5a72e87..a6a3ca8 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/LICENSE-text.html b/LICENSE-text.html index fe11b19..c8874db 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/LICENSE.html b/LICENSE.html index 57c6b2d..7dce28c 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/articles/betadiversity.html b/articles/betadiversity.html index bc569df..9cdaa98 100644 --- a/articles/betadiversity.html +++ b/articles/betadiversity.html @@ -33,7 +33,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/articles/hagis.html b/articles/hagis.html index 6e35e23..35aef99 100644 --- a/articles/hagis.html +++ b/articles/hagis.html @@ -33,7 +33,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/articles/index.html b/articles/index.html index 3d7451d..09e75bf 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/authors.html b/authors.html index eccfab8..28bd08e 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 @@ -125,12 +125,12 @@

Citation

}

McCoy AG, Noel ZA, Sparks AH, Chilvers MI (????). hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity. -doi:10.5281/zenodo.2619820, R package version 3.1.11.9000, https://openplantpathology.github.io/hagis/. +doi:10.5281/zenodo.2619820, R package version 3.1.12, https://openplantpathology.github.io/hagis/. 

@Manual{,
   title = {{hagis}: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity},
   author = {Austin G. McCoy and Zachary A. Noel and Adam H. Sparks and Martin I Chilvers},
-  note = {R package version 3.1.11.9000},
+  note = {R package version 3.1.12},
   url = {https://openplantpathology.github.io/hagis/},
   doi = {10.5281/zenodo.2619820},
 }
diff --git a/index.html b/index.html index d99190a..a54c227 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ hagis - 3.1.11.9000 + 3.1.12 @@ -85,7 +85,6 @@ -

Introduction

@@ -225,8 +224,8 @@

Developers

Dev status

diff --git a/news/index.html b/news/index.html index d7bac5e..dc07eb8 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12
@@ -61,7 +61,12 @@

Changelog

-

hagis (development version)

+

hagis 3.1.12

+
+

Bug fixes

+

  • Fixes examples in “Beta-diversity Analysis with hagis” vignette to work with new versions of {vegan}

    • +

  • Corrects {vegan} example where R2 was incorrectly reported.

    • +

hagis 3.1.112023-09-06

diff --git a/pkgdown.yml b/pkgdown.yml index a22b4c2..ed711ea 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,5 +4,5 @@ pkgdown_sha: ~ articles: betadiversity: betadiversity.html hagis: hagis.html -last_built: 2024-05-16T03:15Z +last_built: 2024-05-16T03:57Z diff --git a/reference/P_sojae_survey.html b/reference/P_sojae_survey.html index 77cb8e4..c7061ac 100644 --- a/reference/P_sojae_survey.html +++ b/reference/P_sojae_survey.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12
diff --git a/reference/autoplot.hagis.complexities.html b/reference/autoplot.hagis.complexities.html index 3786a46..8d2214b 100644 --- a/reference/autoplot.hagis.complexities.html +++ b/reference/autoplot.hagis.complexities.html @@ -20,7 +20,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/reference/autoplot.hagis.gene.summary.html b/reference/autoplot.hagis.gene.summary.html index f59f024..799ba4a 100644 --- a/reference/autoplot.hagis.gene.summary.html +++ b/reference/autoplot.hagis.gene.summary.html @@ -18,7 +18,7 @@ hagis - 3.1.11.9000 + 3.1.12 diff --git a/reference/calculate_complexities.html b/reference/calculate_complexities.html index ce7a7b0..edab3df 100644 --- a/reference/calculate_complexities.html +++ b/reference/calculate_complexities.html @@ -17,7 +17,7 @@ hagis - 3.1.11.9000 + 3.1.12 @@ -102,8 +102,7 @@

Arguments

Value

-

calculate_complexities returns an object of class -hagis.complexities.

+

An object of class hagis.complexities.

An object of class hagis.complexities is a list containing the following diff --git a/reference/calculate_diversities.html b/reference/calculate_diversities.html index dfdad5a..b14bd58 100644 --- a/reference/calculate_diversities.html +++ b/reference/calculate_diversities.html @@ -45,7 +45,7 @@ hagis - 3.1.11.9000 + 3.1.12 @@ -155,7 +155,10 @@

Arguments

Value

-

hagis.diversities object containing