balanced.specaccum: Balanced Species Accumulation Curves

Description Usage Arguments Details Value Author(s) References Examples

Description

Provides species accumulation results calculated from balanced (equal subsample sizes) subsampling from each stratum. Sites can be accumulated in a randomized way, or alternatively sites belonging to the same stratum can be kept together Results are in the same format as specaccum and can be plotted with plot.specaccum (vegan).

Usage

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balanced.specaccum(comm, permutations=100, strata=strata, grouped=TRUE, 
    reps=0, scale=NULL)

Arguments

comm

Community data frame with sites as rows, species as columns and species abundance as cell values.

permutations

Number of permutations to calculate the species accumulation curve.

strata

Categorical variable used to specify strata.

grouped

Should sites from the same stratum be kept together (TRUE) or not.

reps

Number of subsamples to be taken from each stratum (see details).

scale

Quantitative variable used to scale the sampling effort (see details).

Details

This function provides an alternative method of obtaining species accumulation results as provided by specaccum and accumresult.

Balanced sampling is achieved by randomly selecting the same number of sites from each stratum. The number of sites selected from each stratum is determined by reps. Sites are selected from strata with sample sizes larger or equal than reps. In case that reps is smaller than 1 (default: 0), then the number of sites selected from each stratum is equal to the smallest sample size of all strata. Sites from the same stratum can be kept together (grouped=TRUE) or the order of sites can be randomized (grouped=FALSE).

The results can be scaled by the average accumulation of a quantitative variable (default is number of sites), as in accumresult (hint: add the abundance of each site to the environmental data frame to scale accumulation results by mean abundance). When sites are not selected from all strata, then the average is calculated only for the strata that provided sites.

Value

The functions provide alternative methods of obtaining species accumulation curve results, although results are similar as obtained by functions specaccum and accumresult.

Author(s)

Roeland Kindt (World Agroforestry Centre)

References

Kindt, R., Kalinganire, A., Larwanou, M., Belem, M., Dakouo, J.M., Bayala, J. & Kaire, M. (2008) Species accumulation within landuse and tree diameter categories in Burkina Faso, Mali, Niger and Senegal. Biodiversity and Conservation. 17: 1883-1905.

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

https://www.worldagroforestry.org/output/tree-diversity-analysis

Examples

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library(vegan)
data(dune.env)
data(dune)

# not balancing species accumulation
Accum.orig <- specaccum(dune)
Accum.orig

# randomly sample 3 quadrats from each stratum of Management
Accum.1 <- balanced.specaccum(dune, strata=dune.env$Management, reps=3)
Accum.1

# scale results by number of trees per quadrat
dune.env$site.totals <- apply(dune,1,sum)
Accum.2 <- balanced.specaccum(dune, strata=dune.env$Management, reps=3, scale=dune.env$site.totals)
Accum.2

Example output

Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
BiodiversityR 2.11-1: Use command BiodiversityRGUI() to launch the Graphical User Interface; 
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)

Warning message:
no DISPLAY variable so Tk is not available 
Species Accumulation Curve
Accumulation method: exact
Call: specaccum(comm = dune) 

                                                                            
Sites    1.000000  2.000000  3.000000  4.000000  5.000000  6.000000  7.00000
Richness 9.850000 15.110526 18.510526 20.937461 22.754321 24.149587 25.23956
sd       2.351064  1.876385  1.572271  1.446958  1.390159  1.353035  1.31648
                                                                             
Sites     8.000000  9.000000 10.000000 11.000000 12.000000 13.000000 14.00000
Richness 26.103548 26.798244 27.364962 27.833984 28.227546 28.562036 28.84964
sd        1.274903  1.228201  1.176341  1.119344  1.056454  0.987409  0.91160
                                                            
Sites    15.000000 16.000000 17.00000 18.000000 19.000000 20
Richness 29.099587 29.319092 29.51403 29.689474 29.850000 30
sd        0.828689  0.738092  0.63339  0.513971  0.357071  0
Species Accumulation Curve
Accumulation method: balanced species accumulation
Call: balanced.specaccum(comm = dune, strata = dune.env$Management,      reps = 3) 

                                                                          
Sites     1.000000  2.000000  3.000000  4.000000  5.00  6.000000  7.000000
Richness 10.010000 14.670000 17.070000 20.210000 22.19 23.250000 24.510000
sd        2.315931  2.300878  2.001287  1.903187  1.90  1.871503  1.833994
                                                         
Sites     8.000000  9.000000 10.000000 11.000000 12.00000
Richness 25.380000 26.000000 26.880000 27.480000 27.84000
sd        1.790999  1.632993  1.380089  1.068181  0.96106
Species Accumulation Curve
Accumulation method: balanced species accumulation
Call: balanced.specaccum(comm = dune, strata = dune.env$Management,      reps = 3, scale = dune.env$site.totals) 

                                                                              
Sites    35.1917 70.3833 105.5750 140.7667 175.9583 211.1500 246.3417 281.5333
Richness  9.9900 14.4700  16.8700  19.9100  22.1400  23.3100  24.7600  25.6100
sd        2.4433  2.1670   1.8459   2.0156   1.9229   2.0385   1.8264   1.7690
                                            
Sites    316.7250 351.9167 387.1083 422.3000
Richness  26.3100  26.9900  27.6700  28.0000
sd         1.7332   1.5341   1.3108   1.0825

BiodiversityR documentation built on April 20, 2021, 5:07 p.m.