estimateD: Compute species diversity with a particular of sample...

Description Usage Arguments Value Examples

View source: R/invChat.R

Description

estimateD: computes species diversity (Hill numbers with q = 0, 1 and 2) with a particular user-specified level of sample size or sample coverage.

Usage

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estimateD(x, datatype = "abundance", base = "size", level = NULL,
  conf = 0.95)

Arguments

x

a data.frame or list of species abundances or incidence frequencies.
If datatype = "incidence", then the first entry of the input data must be total number of sampling units, followed by species incidence frequencies in each column or list.

datatype

data type of input data: individual-based abundance data (datatype = "abundance"), sampling-unit-based incidence frequencies data (datatype = "incidence_freq") or species by sampling-units incidence matrix (datatype = "incidence_raw").

base

comparison base: sample-size-based (base="size") or coverage-based
(base="coverage").

level

an value specifying a particular sample size or a number (between 0 and 1) specifying a particular value of sample coverage. If base="size" and level=NULL, then this function computes the diversity estimates for the minimum sample size among all sites. If base="coverage" and level=NULL, then this function computes the diversity estimates for the minimum sample coverage among all sites.

conf

a positive number < 1 specifying the level of confidence interval, default is 0.95. Remove C.I. by setting conf=NULL.

Value

a data.frame of species diversity table including the sample size, sample coverage, method (rarefaction or extrapolation), and diversity estimates with q = 0, 1, and 2 for the user-specified sample size or sample coverage.

Examples

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data(spider)
estimateD(spider, "abundance", base="size", level=NULL, conf=0.95)
estimateD(spider, "abundance", base="coverage", level=NULL, conf=0.95)

data(ant)
estimateD(ant, "incidence_freq", base="coverage", level=0.985, conf=NULL)

Example output

     site   m       method order    SC     qD qD.LCL qD.UCL
1 Girdled 168     observed     0 0.929 26.000 20.706 31.294
2 Girdled 168     observed     1 0.929 12.060  9.967 14.152
3 Girdled 168     observed     2 0.929  7.840  6.140  9.540
4  Logged 168 interpolated     0 0.927 31.707 27.157 36.258
5  Logged 168 interpolated     1 0.927 13.745 11.138 16.353
6  Logged 168 interpolated     2 0.927  6.685  5.239  8.131
     site   m       method order    SC     qD qD.LCL qD.UCL
1 Girdled 168     observed     0 0.929 26.000 21.624 30.376
2 Girdled 168     observed     1 0.929 12.060  9.957 14.162
3 Girdled 168     observed     2 0.929  7.840  6.081  9.599
4  Logged 175 interpolated     0 0.929 32.213 27.582 36.844
5  Logged 175 interpolated     1 0.929 13.820 11.417 16.224
6  Logged 175 interpolated     2 0.929  6.694  4.932  8.456
    site   t       method    SC   q = 0   q = 1  q = 2
1   h50m 327 interpolated 0.985 197.463  78.051 50.461
2  h500m 343 extrapolated 0.985 268.753 103.844 64.759
3 h1070m 159 extrapolated 0.985 123.617  59.592 41.775
4 h1500m 126 interpolated 0.985  50.482  26.249 18.649
5 h2000m 105 interpolated 0.985  12.917   7.712  5.795

iNEXT documentation built on July 10, 2018, 1:04 a.m.