Daily Update

R/list.txt

@@ -167,16 +167,16 @@
 "xiangyun.rbind.io/index.xml","2025-01-09"
 "feeds.feedburner.com/ProfessorRobJHyndman","2025-01-09"
 "robjhyndman.com/index.xml","2025-01-09"
-"https://asa-blog.netlify.app/index.xml","2025-01-09"
 "freakonometrics.hypotheses.org/feed","2025-01-10"
 "https://yangzhang.site/feed_rss_updated.xml","2025-01-12"
 "http://anotherdayu.com/?feed=rss","2025-01-13"
 "anotherdayu.com/feed/","2025-01-13"
-"dirk.eddelbuettel.com/blog/index.rss","2025-01-13"
 "s0521.github.io/cn/index.xml","2025-01-14"
-"flowingdata.com/feed","2025-01-14"
-"https://www.r-bloggers.com/feed","2025-01-14"
-"www.robinlovelace.net/index.xml","2025-01-14"
 "jihongzhang.org/index.xml","2025-01-14"
-"statmodeling.stat.columbia.edu/feed/","2025-01-14"
-"andrewgelman.com/feed/","2025-01-14"
+"https://asa-blog.netlify.app/index.xml","2025-01-15"
+"dirk.eddelbuettel.com/blog/index.rss","2025-01-15"
+"flowingdata.com/feed","2025-01-15"
+"https://www.r-bloggers.com/feed","2025-01-15"
+"www.robinlovelace.net/index.xml","2025-01-15"
+"statmodeling.stat.columbia.edu/feed/","2025-01-15"
+"andrewgelman.com/feed/","2025-01-15"

content/post/-p-kraken-16s-its.md

@@ -0,0 +1,16 @@
+---
+title: 使用Kraken进行16S/ITS物种注释（超快）
+date: '2025-01-14'
+linkTitle: /p/kraken-16s-its/
+source: Asa's blog
+description: |-
+  <img src="/p/kraken-16s-its/images/k16s1.png" alt="Featured image of post 使用Kraken进行16S/ITS物种注释（超快）" /><h2 id="introduction">Introduction</h2>
+  <p>上次记录了一下qiime2的<a class="link" href="../amplicon-workflow" >扩增子分析流程</a>。但是实际使用时，在最后一步物种注释时卡住了，如果使用常用的<code>feature-classifier</code>方法，我尝试使用unite数据库鉴定了100条ITS序列，居然用了半个小时！尴尬的是，我有整整10万条ASV序列，这得跑到猴年马月。我想到做宏基因组时，千万级数量的reads用kraken做物种注释也不需要这么久，肯定有快的方法的。</p>
+  <p>然后发现Kraken用于16S已经有文章了：
+  Lu, J., Salzberg, S.L. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2. Microbiome 8, 124 (2020). <a class="link" ...
+disable_comments: true
+---
+<img src="/p/kraken-16s-its/images/k16s1.png" alt="Featured image of post 使用Kraken进行16S/ITS物种注释（超快）" /><h2 id="introduction">Introduction</h2>
+<p>上次记录了一下qiime2的<a class="link" href="../amplicon-workflow" >扩增子分析流程</a>。但是实际使用时，在最后一步物种注释时卡住了，如果使用常用的<code>feature-classifier</code>方法，我尝试使用unite数据库鉴定了100条ITS序列，居然用了半个小时！尴尬的是，我有整整10万条ASV序列，这得跑到猴年马月。我想到做宏基因组时，千万级数量的reads用kraken做物种注释也不需要这么久，肯定有快的方法的。</p>
+<p>然后发现Kraken用于16S已经有文章了：
+Lu, J., Salzberg, S.L. Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2. Microbiome 8, 124 (2020). <a class="link" ...

content/post/dirk-eddelbuettel-com-blog-2025-01-14-rprotobuf-0-4-23.md

@@ -0,0 +1,30 @@
+---
+title: 'RProtoBuf 0.4.23 on CRAN: Mulitple Updates'
+date: '2025-01-14'
+linkTitle: http://dirk.eddelbuettel.com/blog/2025/01/14#rprotobuf_0.4.23
+source: 'Thinking inside the box   '
+description: |2-
+   <p>A new maintenance release 0.4.23 of <a
+  href="https://dirk.eddelbuettel.com/code/rprotobuf.html">RProtoBuf</a>
+  arrived on <a href="https://cran.r-project.org">CRAN</a> earlier today,
+  about one year after the <a
+  href="https://dirk.eddelbuettel.com/blog/2024/01/21#rprotobuf_0.4.22">previous
+  update</a>. <a
+  href="https://dirk.eddelbuettel.com/code/rprotobuf.html">RProtoBuf</a>
+  provides <a href="https://www.r-project.org">R</a> with bindings for the
+  <a href="https://github.com/google/protobuf">Google Protocol Buffers
+  (“ProtoBuf”)</a> data encoding and serialization library used and
+  released by Google, and  ...
+disable_comments: true
+---
+ <p>A new maintenance release 0.4.23 of <a
+href="https://dirk.eddelbuettel.com/code/rprotobuf.html">RProtoBuf</a>
+arrived on <a href="https://cran.r-project.org">CRAN</a> earlier today,
+about one year after the <a
+href="https://dirk.eddelbuettel.com/blog/2024/01/21#rprotobuf_0.4.22">previous
+update</a>. <a
+href="https://dirk.eddelbuettel.com/code/rprotobuf.html">RProtoBuf</a>
+provides <a href="https://www.r-project.org">R</a> with bindings for the
+<a href="https://github.com/google/protobuf">Google Protocol Buffers
+(“ProtoBuf”)</a> data encoding and serialization library used and
+released by Google, and  ...

content/post/flowingdata-com-2025-01-14-distribution-of-days-that-were-hotter-than-average.md

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+---
+title: Distribution of days that were hotter than average
+date: '2025-01-14'
+linkTitle: https://flowingdata.com/2025/01/14/distribution-of-days-that-were-hotter-than-average/
+source: FlowingData
+description: <p><a href="https://flowingdata.com/2025/01/14/distribution-of-days-that-were-hotter-than-average/"><img
+  src="https://flowingdata.com/wp-content/uploads/2025/01/hotter-days-bbc-750x1414.png"
+  style="max-width:100%;height:auto" /></a></p>BBC went with the gradient-filled frequency
+  trails to show the distribution of daily&#8230;<p><strong>Tags:</strong> <a href="https://flowingdata.com/tag/bbc/"
+  rel="tag">BBC</a>, <a href="https://flowingdata.com/tag/climate-change/" rel="tag">climate
+  change</a>, <a href="https://flowingdata.com/tag/global-warming/" rel="tag">global
+  ...
+disable_comments: true
+---
+<p><a href="https://flowingdata.com/2025/01/14/distribution-of-days-that-were-hotter-than-average/"><img src="https://flowingdata.com/wp-content/uploads/2025/01/hotter-days-bbc-750x1414.png" style="max-width:100%;height:auto" /></a></p>BBC went with the gradient-filled frequency trails to show the distribution of daily&#8230;<p><strong>Tags:</strong> <a href="https://flowingdata.com/tag/bbc/" rel="tag">BBC</a>, <a href="https://flowingdata.com/tag/climate-change/" rel="tag">climate change</a>, <a href="https://flowingdata.com/tag/global-warming/" rel="tag">global ...

content/post/flowingdata-com-2025-01-14-earth-was-hotter-than-ever-again.md

@@ -0,0 +1,15 @@
+---
+title: Earth was hotter than ever, again
+date: '2025-01-14'
+linkTitle: https://flowingdata.com/2025/01/14/earth-was-hotter-than-ever-again/
+source: FlowingData
+description: <p><a href="https://flowingdata.com/2025/01/14/earth-was-hotter-than-ever-again/"><img
+  src="https://flowingdata.com/wp-content/uploads/2025/01/warning-threshold-NYT-750x461.png"
+  style="max-width:100%;height:auto" /></a></p>This is some good step charting by
+  Mira Rojanasakul for the New York&#8230;<p><strong>Tags:</strong> <a href="https://flowingdata.com/tag/climate-change/"
+  rel="tag">climate change</a>, <a href="https://flowingdata.com/tag/global-warming/"
+  rel="tag">global warming</a>, <a href="https://flowingdata.com/tag/new-york-times/"
+  rel="tag">New York ...
+disable_comments: true
+---
+<p><a href="https://flowingdata.com/2025/01/14/earth-was-hotter-than-ever-again/"><img src="https://flowingdata.com/wp-content/uploads/2025/01/warning-threshold-NYT-750x461.png" style="max-width:100%;height:auto" /></a></p>This is some good step charting by Mira Rojanasakul for the New York&#8230;<p><strong>Tags:</strong> <a href="https://flowingdata.com/tag/climate-change/" rel="tag">climate change</a>, <a href="https://flowingdata.com/tag/global-warming/" rel="tag">global warming</a>, <a href="https://flowingdata.com/tag/new-york-times/" rel="tag">New York ...

content/post/statmodeling-stat-columbia-edu-2025-01-14-genre-fiction-some-genres-are-cumulative-and-some-are-not.md

@@ -0,0 +1,13 @@
+---
+title: 'Genre fiction:  Some genres are cumulative and some are not.'
+date: '2025-01-14'
+linkTitle: https://statmodeling.stat.columbia.edu/2025/01/14/genre-fiction-some-genres-are-cumulative-and-some-are-not/
+source: Statistical Modeling, Causal Inference, and Social Science
+description: I’ve been reading some books about the history of twentieth-century
+  mystery novels and science fiction stories, and one thing that struck me was that
+  each of these genres had a sense of continuity. If you used a gimmick in a …
+  <a href="https://statmodeling.stat.columbia.edu/2025/01/14/genre-fiction-some-genres-are-cumulative-and-some-are-not/">Continue
+  reading <span class="meta-nav">&#8594;</span></a> ...
+disable_comments: true
+---
+I&#8217;ve been reading some books about the history of twentieth-century mystery novels and science fiction stories, and one thing that struck me was that each of these genres had a sense of continuity. If you used a gimmick in a &#8230; <a href="https://statmodeling.stat.columbia.edu/2025/01/14/genre-fiction-some-genres-are-cumulative-and-some-are-not/">Continue reading <span class="meta-nav">&#8594;</span></a> ...

content/post/www-r-bloggers-com-2025-01-basic-data-structures-in-r-vectors-matrices-and-data-frames.md

@@ -0,0 +1,16 @@
+---
+title: 'Basic Data Structures in R: Vectors, Matrices, and Data Frames'
+date: '2025-01-14'
+linkTitle: https://www.r-bloggers.com/2025/01/basic-data-structures-in-r-vectors-matrices-and-data-frames/
+source: R-bloggers
+description: |-
+  <div style = "width:60%; display: inline-block; float:left; "> IntroductionIn the world of data analysis and statistical computing, R stands out as a powerful and versatile language. Its ability to handle complex data operations with ease makes it a favorite among data scientists, statisticians, and researchers. A...</div>
+  <div style = "width: 40%; display: inline-block; float:right;"></div>
+  <div style="clear: both;"></div>
+  <strong>Continue reading</strong>: <a href="https://www.r-bloggers.com/2025/01/basic-data-structures-in-r-vectors-matrices-and-data-frames/">Basic Data Structures in R: ...
+disable_comments: true
+---
+<div style = "width:60%; display: inline-block; float:left; "> IntroductionIn the world of data analysis and statistical computing, R stands out as a powerful and versatile language. Its ability to handle complex data operations with ease makes it a favorite among data scientists, statisticians, and researchers. A...</div>
+<div style = "width: 40%; display: inline-block; float:right;"></div>
+<div style="clear: both;"></div>
+<strong>Continue reading</strong>: <a href="https://www.r-bloggers.com/2025/01/basic-data-structures-in-r-vectors-matrices-and-data-frames/">Basic Data Structures in R: ...

content/post/www-r-bloggers-com-2025-01-understanding-machine-learning-and-data-science.md

@@ -0,0 +1,16 @@
+---
+title: Understanding Machine Learning and Data Science
+date: '2025-01-14'
+linkTitle: https://www.r-bloggers.com/2025/01/understanding-machine-learning-and-data-science/
+source: R-bloggers
+description: |-
+  <p>The post Understanding Machine Learning and Data Science appeared first on Data Science Tutorials<br />
+  Unravel the Future: Dive Deep into the World of Data Science Today! Data Science Tutorials.<br />
+  Understanding Machine Learning and Data Science, In today’s digital age, the terms “Machine Learning” and “Data Science” have become buzzwords, ...</p>
+  <strong>Continue reading</strong>: <a href="https://www.r-bloggers.com/2025/01/understanding-machine-learning-and-data-science/">Understanding Machine Learning and Data ...
+disable_comments: true
+---
+<p>The post Understanding Machine Learning and Data Science appeared first on Data Science Tutorials<br />
+Unravel the Future: Dive Deep into the World of Data Science Today! Data Science Tutorials.<br />
+Understanding Machine Learning and Data Science, In today’s digital age, the terms “Machine Learning” and “Data Science” have become buzzwords, ...</p>
+<strong>Continue reading</strong>: <a href="https://www.r-bloggers.com/2025/01/understanding-machine-learning-and-data-science/">Understanding Machine Learning and Data ...