Answers.Body: <p>I cannot access the book, it might be an older version or there are some steps in between. The screen shot doesn't help.</p>
  <p>If you look at the <a href="https://cran.r-project.org/web/packages/phangorn/vignettes/phangorn-specials.pdf" rel="nofollow noreferrer">vignette</a> and the error, what you need to provide is a matrix of characters with defined row names, for example:</p>
  <pre><code>set.seed(111)
  x = sample(letters,100,replace=TRUE)
  phyDat(matrix(x),&quot;USER&quot;,levels=unique(x))
  
  Error in phyDat.default(data, levels = levels, return.index = return.index,  : 
    data object must contain taxa names
  
  mat = matrix(x,10,10,dimnames=list(paste0(&quot;t&quot;,1:10),NULL))
  phyDat(mat,&quot;USER&quot;,levels=unique(x))
  10 sequences with 10 character and 10 different site patterns.
  The states are n t s o y e c h z q m j d o h n z y x p q g u o a i h y c g t d f y t d f e u e f d i j r z x w u m a j p j g d t q y v o x p m s o z x z a y j z r u s a y k l f g l f r i l r f m t t e f x v f g q j 
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-12T19:49:29.510Z
Answers.LastActivityDate: 2020-08-12T19:49:29.510Z
Answers.UserDisplayName: StupidWolf
Body: <p>I am following an example from ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis.</p>
  <p>He is doing:</p>
  <p><a href="https://i.sstatic.net/7uTVB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/7uTVB.png" alt="enter image description here" /></a></p>
  <p>I am doing pretty much the same:</p>
  <pre><code>x=c('garras','garras','garras', 'tejido','tejido','tejido')
  y &lt;- phyDat(matrix(x), &quot;USER&quot;, levels = unique(x))
  </code></pre>
  <p>but I get:</p>
  <blockquote>
  <p>Error in phyDat.default(data, levels = levels, return.index =
  return.index, : data object must contain taxa names</p>
  </blockquote>
  <p>Screenshot:</p>
  <p><a href="https://i.sstatic.net/bIRKC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/bIRKC.png" alt="enter image description here" /></a></p>
  <p>What am I doing wrong? how come the example from the book works...</p>
  
Tags: <r><phylogenetics>
Title: Unable to use phangorn::phyDat
ThreadText: # Unable to use phangorn::phyDat
  
  (Asked by: username_0 on 2020-08-11)
  
  I am following an example from ‘Analysis of Phylogenetics Second Edition and Evolution with R’ from Emmanuel Paradis.
  
  He is doing:
  
  [![enter image description here](https://i.sstatic.net/7uTVB.png)](https://i.sstatic.net/7uTVB.png)
  
  I am doing pretty much the same:
  
  ```
  x=c('garras','garras','garras', 'tejido','tejido','tejido')
  y <- phyDat(matrix(x), "USER", levels = unique(x))
  
  ```
  
  but I get:
  
  > Error in phyDat.default(data, levels = levels, return.index =
  > return.index, : data object must contain taxa names
  
  Screenshot:
  
  [![enter image description here](https://i.sstatic.net/bIRKC.png)](https://i.sstatic.net/bIRKC.png)
  
  What am I doing wrong? how come the example from the book works...
  
  **Tags:** r, phylogenetics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-08-12. Score: 1 | Accepted answer
  
  I cannot access the book, it might be an older version or there are some steps in between. The screen shot doesn't help.
  
  If you look at the [vignette](https://cran.r-project.org/web/packages/phangorn/vignettes/phangorn-specials.pdf) and the error, what you need to provide is a matrix of characters with defined row names, for example:
  
  ```
  set.seed(111)
  x = sample(letters,100,replace=TRUE)
  phyDat(matrix(x),"USER",levels=unique(x))
  
  Error in phyDat.default(data, levels = levels, return.index = return.index,  : 
    data object must contain taxa names
  
  mat = matrix(x,10,10,dimnames=list(paste0("t",1:10),NULL))
  phyDat(mat,"USER",levels=unique(x))
  10 sequences with 10 character and 10 different site patterns.
  The states are n t s o y e c h z q m j d o h n z y x p q g u o a i h y c g t d f y t d f e u e f d i j r z x w u m a j p j g d t q y v o x p m s o z x z a y j z r u s a y k l f g l f r i l r f m t t e f x v f g q j 
  
  ```
  
  
  ---
  
  