nucDiag: Nucleotide diagnostics for species alignments
In spider: Species Identity and Evolution in R

Description Usage Arguments Details Value Author(s) References See Also Examples

Determines the diagnostic nucleotides for each species given in sppVector.

1 2	nucDiag(DNAbin, sppVector) rnucDiag(DNAbin, sppVector, n = 100)

`DNAbin`	An object of class 'DNAbin'.
`sppVector`	The species vector (see `sppVector`).
`n`	The number of pseudoreplicates to perform. Default of 100

These functions provide a means for evaluating the presence of diagnostic nucleotides that distinguish species within an alignment. nucDiag returns the positions of bases corresponding to the definition of pure, simple diagnostic nucleotides given by Sarkar et al (2008).

rnucDiag runs a bootstrapping-style resampling test to evaluate the numbers of diagnostic nucleotides that might be expected by random assortment of specimens.

nucDiag returns a list giving the pure, simple diagnostic nucleotides (i.e. those nucleotides that are fixed within species and different from all other species) for each species in the species vector. A result of integer(0) indicates there are no diagnostic nucleotides for those species.

rnucDiag returns a list containing the following elements:

`min`	The minimum number of diagnostic nucleotides in the sample.
`mean`	The mean number of diagnostic nucleotides in the sample.
`median`	The median number of diagnostic nucleotides in the sample.
`max`	The maximum number of diagnostic nucleotides in the sample.
`rndFreq`	A list of frequency distributions of the number of diagnostic nucleotides in groups formed by 1 sequence, 2 sequences, etc.

Samuel Brown <s_d_j_brown@hotmail.com>

Sarkar, I., Planet, P., & DeSalle, R. (2008). CAOS software for use in character- based DNA barcoding. _Molecular Ecology Resources_ *8* 1256-1259

slideNucDiag

data(anoteropsis)
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
	function(x) paste(x[1], x[2], sep="_"))

nucDiag(anoteropsis, anoSpp)


#To view the nucleotide values 
anoNuc <- nucDiag(anoteropsis, anoSpp)
as.character(anoteropsis[ ,anoNuc[[1]][1] ])



data(sarkar)
sarkarSpp <- substr(dimnames(sarkar)[[1]], 1, 3)
nucDiag(sarkar, sarkarSpp)

## Not run: 
rnucDiag(anoteropsis, anoSpp, n = 100)

## End(Not run)

Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 
Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4
$Artoria_flavimanus
 [1]   4  10  79 106 133 169 218 220 241 289 307

$Artoria_separata
[1]   7  31  40  61  79 232 280 364

$Anoteropsis_adumbrata
[1] 319

$Anoteropsis_aerescens
integer(0)

$Anoteropsis_alpina
[1] 112 169 343

$Anoteropsis_arenivaga
[1]  4 52

$Anoteropsis_blesti
[1] 193 370

$Anoteropsis_canescens
[1] 214

$Anoteropsis_cantuaria
[1] 223 403

$Anoteropsis_flavescens
integer(0)

$Anoteropsis_forsteri
integer(0)

$Anoteropsis_hallae
integer(0)

$Anoteropsis_hilaris
[1] 83

$Anoteropsis_insularis
[1] 73

$Anoteropsis_lacustris
[1]  70 157 286

$Anoteropsis_litoralis
[1]  64 281 325

$Anoteropsis_montana
[1] 166 301

$Anoteropsis_okatainae
[1]  70 247 340

$Anoteropsis_ralphi
[1] 142 178 190

$Anoteropsis_senica
integer(0)

$Anoteropsis_urquharti
[1] 10

$Anoteropsis_westlandica
[1] 34

                         [,1]
Artoria_flavimanus       "a" 
Artoria_separata         "t" 
Anoteropsis_adumbrata_CO "t" 
Anoteropsis_adumbrata_BP "t" 
Anoteropsis_aerescens_MK "t" 
Anoteropsis_aerescens_TK "t" 
Anoteropsis_aerescens_WN "t" 
Anoteropsis_alpina       "t" 
Anoteropsis_arenivaga_NC "c" 
Anoteropsis_arenivaga_MC "c" 
Anoteropsis_blesti       "t" 
Anoteropsis_canescens    "t" 
Anoteropsis_cantuaria    "t" 
Anoteropsis_flavescens   "t" 
Anoteropsis_forsteri     "t" 
Anoteropsis_hallae       "t" 
Anoteropsis_hilaris_CO   "t" 
Anoteropsis_hilaris_AK   "t" 
Anoteropsis_hilaris_MC   "t" 
Anoteropsis_hilaris_SL   "t" 
Anoteropsis_insularis    "t" 
Anoteropsis_lacustris    "t" 
Anoteropsis_litoralis_MC "t" 
Anoteropsis_litoralis_CL "t" 
Anoteropsis_montana      "t" 
Anoteropsis_okatainae    "t" 
Anoteropsis_ralphi       "t" 
Anoteropsis_senica_WD    "t" 
Anoteropsis_senica_TK    "t" 
Anoteropsis_urquharti_MC "t" 
Anoteropsis_urquharti_OL "t" 
Anoteropsis_urquharti_CO "t" 
Anoteropsis_westlandica  "t" 
$AAA
[1] 2

$BBB
[1] 2

$min
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

$mean
  [1] 0.50000000 0.46666667 0.33333333 1.11764706 0.85714286 0.53846154
  [7] 1.00000000 0.90000000 0.41176471 0.41176471 0.81250000 0.81250000
 [13] 1.17647059 0.58823529 0.75000000 1.15000000 1.18750000 0.40000000
 [19] 1.41176471 0.23076923 0.05882353 0.70588235 0.29411765 0.28571429
 [25] 0.06666667 0.20000000 0.38888889 0.05882353 0.16666667 0.68750000
 [31] 1.11764706 0.50000000 1.13333333 0.94117647 0.23076923 0.92307692
 [37] 0.17647059 0.37500000 0.46666667 1.07142857 0.13333333 0.52631579
 [43] 0.38461538 0.42105263 0.42857143 0.58823529 0.64285714 0.73333333
 [49] 0.94117647 1.00000000 0.47058824 0.08333333 1.00000000 0.18750000
 [55] 0.53333333 0.68750000 0.88888889 0.75000000 0.37500000 0.35294118
 [61] 1.05882353 0.93333333 0.29411765 0.53846154 1.62500000 0.15384615
 [67] 0.42857143 0.23529412 0.35294118 0.84210526 0.81250000 0.38888889
 [73] 1.00000000 0.27777778 0.20000000 0.60000000 0.83333333 0.27272727
 [79] 0.80000000 0.06250000 0.23076923 0.81250000 0.46666667 1.62500000
 [85] 0.18750000 0.07692308 0.94117647 0.81250000 0.66666667 1.06250000
 [91] 1.73684211 0.56250000 0.33333333 0.38461538 0.35714286 0.46666667
 [97] 0.40000000 0.62500000 1.00000000 0.21428571

$median
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [75] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

$max
  [1]  3  3  3 11  8  3 11  8  3  3  8  3 11  3  3 11  8  3 11  1  1  8  3  2  1
 [26]  3  3  1  3  8 11  3 11 11  3 11  2  2  3  8  1  3  2  3  3  3  8 11  8 11
 [51]  3  1  8  2  3  8 11  8  3  3 11  8  3  3 11  1  3  1  3  8  3  3 11  3  2
 [76]  3 11  3  8  1  3  8  3 11  1  1  8 11  3 11 11  3  2  3  3  3  2  8 11  2

$rndFreq
$rndFreq$`1`

  0   1   2   3   8  11 
530  70  38  47   9   8 

$rndFreq$`2`

  0   1   2   3   8  11 
337  32  19  20   6   7 

$rndFreq$`3`

  0   1   2   3   8  11 
187  22  14  15   4   4 

$rndFreq$`4`

 0  1  2  3  8 11 
99 16  6  6  1  1 

$rndFreq$`5`

 0  1  2  3 11 
34  5  3  2  1 

$rndFreq$`6`

 0  1  2  3 
21  1  2  1 

$rndFreq$`7`

0 1 2 3 
6 1 1 1 

$rndFreq$`8`

0 
2 

$rndFreq$`9`

0 
3 

$rndFreq$`10`

0 
1 

$rndFreq$`11`

0 
1