strep: Streptococcus data set.

In clst: Classification by local similarity threshold

Description

Square matrices decsribing pairwise distances among 16s rRNA sequences.

Usage

data(strep)

Format

List of 5
 $ dmat1 : num [1:150, 1:150] 0 5.81 8.38 10.28 10.64 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
 $ dmat2 : num [1:150, 1:150] 0 5.09 3.82 7.21 7.59 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
 $ dmat3 : num [1:150, 1:150] 0 5.63 5.81 8.77 9.14 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
  .. ..$ : chr [1:150] "197" "199" "207" "208" ...
 $ taxa  : Factor w/ 50 levels "Streptococcus acidominimus",..: 31 44 26 4 4 31 32 39 42 31 ...
 $ abbrev: Factor w/ 50 levels "S acidominimus",..: 31 44 26 4 4 31 32 39 42 31 ...

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(strep)

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