actino: Actinomyces data set

In clst: Classification by local similarity threshold

Description

Square matrices decsribing pairwise distances among 16s rRNA sequences.

Usage

data(actino)

Format

List of 5
 $ dmat1 : num [1:146, 1:146] 0 0.763 1.25 10.345 12.771 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
 $ dmat2 : num [1:146, 1:146] 0 0.574 1.044 5.669 8.409 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
 $ dmat3 : num [1:146, 1:146] 0 0.763 1.25 8.571 11.233 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
  .. ..$ : chr [1:146] "200" "201" "202" "203" ...
 $ taxa  : Factor w/ 33 levels "Actinomyces bowdenii",..: 12 12 12 23 20 20 8 22 12 20 ...
 $ abbrev: Factor w/ 33 levels "A bowdenii","A canis",..: 12 12 12 23 20 20 8 22 12 20 ...

Details

The matrices $dmat1, dmat2, and dmat3 contain percent nucleotide difference with indels penalized heavily, little, and somewhat, respectively.

$taxa is a factor of species names; abbreviations of the same names are found in $abbrev.

Examples

data(actino)

clst documentation built on Nov. 8, 2020, 5:41 p.m.