Fix formatting and remove trailing spaces #1289
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Major fixes were misplaced backticks, which interfere with rendering. Minor changes are removal of trailing space.
erictleung
commented
Jan 1, 2020
| @@ -74,7 +74,7 @@ theme_set(theme_bw()) | |||
| See the [microbio_me_qiime tutorial](http://joey711.github.io/phyloseq/download-microbio.me.html) for more details and examples downloading and importing into phyloseq/R directly from this public database. | |||
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| ## Included Data | |||
| To facilitate testing and exploration of tools in phyloseq, this package includes example data from published studies. Many of the examples in this vignette use either the [Global Patterns](http://www.pnas.org/content/early/2010/06/02/1000080107) or `enterotype` datasets as source data. The [Global Patterns](http://www.pnas.org/content/early/2010/06/02/1000080107) data was described in a [2011 article in PNAS](http://www.pnas.org/content/early/2010/06/02/1000080107)([Caporaso 2011](http://www.pnas.org/content/early/2010/06/02/1000080107)), and compares the microbial communities of 25 environmental samples and three known "mock communities" --- a total of 9 sample types --- at a depth averaging 3.1 million reads per sample. The [human enterotype dataset](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html) was described in a [2011 article in Nature](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html) ([Arumugam 2011](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html)), which compares the faecal microbial communities from 22 subjects using complete shotgun DNA sequencing. The authors further compare these microbial communities with the faecal communities of subjects from other studies, for a total of 280 faecal samples / subjects, and 553 genera. Sourcing data from different studies invariable leads to gaps in the data for certain variables, and this is easily handled by `R's core `NA features. | |||
| To facilitate testing and exploration of tools in phyloseq, this package includes example data from published studies. Many of the examples in this vignette use either the [Global Patterns](http://www.pnas.org/content/early/2010/06/02/1000080107) or `enterotype` datasets as source data. The [Global Patterns](http://www.pnas.org/content/early/2010/06/02/1000080107) data was described in a [2011 article in PNAS](http://www.pnas.org/content/early/2010/06/02/1000080107)([Caporaso 2011](http://www.pnas.org/content/early/2010/06/02/1000080107)), and compares the microbial communities of 25 environmental samples and three known "mock communities" --- a total of 9 sample types --- at a depth averaging 3.1 million reads per sample. The [human enterotype dataset](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html) was described in a [2011 article in Nature](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html) ([Arumugam 2011](http://www.nature.com/nature/journal/v473/n7346/full/nature09944.html)), which compares the faecal microbial communities from 22 subjects using complete shotgun DNA sequencing. The authors further compare these microbial communities with the faecal communities of subjects from other studies, for a total of 280 faecal samples / subjects, and 553 genera. Sourcing data from different studies invariable leads to gaps in the data for certain variables, and this is easily handled by R's core `NA` features. | |||
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GitHub's diff here is difficult to see. The change here is in the last sentence in the last four to five words.
erictleung
commented
Jan 1, 2020
| distance(esophagus, "wunifrac") # weighted UniFrac | ||
| distance(esophagus, "jaccard") # vegdist jaccard | ||
| distance(esophagus, "g") # betadiver method option "g" | ||
| ``` | ||
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| ### UniFrac and weighted UniFrac | ||
| UniFrac is a recently-defined~\cite{Lozupone:2005gn and popular distance metric to summarize the difference between pairs of ecological communities. All UniFrac variants use a phylogenetic tree of the relationship among taxa as central information to calculating the distance between two samples/communities. An unweighted UniFrac distance matrix only considers the presence/absence of taxa, while weighted UniFrac accounts for the relative abundance of taxa as well as their phylogenetic distance. Prior to phyloseq, a non-parallelized, non-Fast implementation of the unweighted UniFrac was available in \R{ packages (`picante::unifrac`~\cite{Kembel:2010ft). In the phyloseq package we provide optionally-parallelized implementations of Fast UniFrac~\cite{Hamady:2009fk (both weighted and unweighted, with plans for additional UniFrac variants), all of which return a sample-wise distance matrix from any `phyloseq-class object that contains a phylogenetic tree component. | ||
| UniFrac is a recently-defined~\cite{Lozupone:2005gn and popular distance metric to summarize the difference between pairs of ecological communities. All UniFrac variants use a phylogenetic tree of the relationship among taxa as central information to calculating the distance between two samples/communities. An unweighted UniFrac distance matrix only considers the presence/absence of taxa, while weighted UniFrac accounts for the relative abundance of taxa as well as their phylogenetic distance. Prior to phyloseq, a non-parallelized, non-Fast implementation of the unweighted UniFrac was available in \R{ packages (`picante::unifrac`~\cite{Kembel:2010ft). In the phyloseq package we provide optionally-parallelized implementations of Fast UniFrac~\cite{Hamady:2009fk (both weighted and unweighted, with plans for additional UniFrac variants), all of which return a sample-wise distance matrix from any `phyloseq-class` object that contains a phylogenetic tree component. |
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GitHub's diff here is difficult to see. The change here is in the last sentence in the last eight or ten words. Plus a trailing space was removed.
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Major fixes were misplaced backticks, which interfere with rendering.
Minor changes are removal of trailing space.