pis: Number of Potentially-Informative Sites

Description Usage Arguments Value Author(s) Examples

Description

This function returns the number or positions of potentially-informative (parsimony-informative, phylogenetically-informative) sites in DNA sequence alignment.

Usage

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pis(x, what = "fraction", use.ambiguities = FALSE)

Arguments

x

An object of class DNAbin.

what

Either of "absolute", "fraction", or "index", which will return the absolute number, the relative number or the indeces of the potentially-informative sites.

use.ambiguities

Not yet available.

Value

Numeric (depending on what, the number, fraction, or indices of potentially-informative nucleotide sites).

Author(s)

Christoph Heibl

Examples

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# example data:
# -------------
data(ips.16S)	

# number of potentially-informative sites:
# ----------------------------------------
pis(ips.16S, what = "abs")
	
# proportion of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "frac")

# indeces of potentially-informative sites:
# --------------------------------------------
pis(ips.16S, what = "ind")

Example output

Loading required package: ape
Loading required package: colorspace
Loading required package: XML
[1] 138
[1] 36.7
  [1]   3   6  13  24  45  52  59  60  68  74  85  88  89  90  91  92 101 102
 [19] 103 104 105 107 108 109 111 113 117 131 133 145 147 148 149 151 168 178
 [37] 181 182 183 185 186 187 188 190 191 192 193 194 195 196 197 198 199 200
 [55] 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218
 [73] 220 221 222 223 224 225 226 227 228 229 230 231 232 235 236 237 247 248
 [91] 249 257 258 259 260 261 272 273 276 277 278 279 280 281 282 283 284 286
[109] 287 288 292 293 296 297 298 299 300 301 302 314 317 318 319 320 321 323
[127] 324 331 332 333 334 338 345 359 367 369 374 375

ips documentation built on July 4, 2019, 5:04 p.m.