# Alternative Species Accumulation Curve Results

### Description

Provides alternative methods of obtaining species accumulation results than provided by functions `specaccum`

and `plot.specaccum`

(vegan).

### Usage

1 2 3 4 5 6 7 8 | ```
accumresult(x,y="",factor="",level,scale="",method="exact",permutations=100,
conditioned=T, gamma="boot", ...)
accumplot(xr,addit=F,labels="",col=1,ci=2,pch=1,type="p",cex=1,xlim=c(1,xmax),
ylim=c(1,rich),xlab="sites",ylab="species richness",...)
accumcomp(x,y="",factor,scale="",method="exact",permutations=100,
conditioned=T, gamma="boot",plotit=T,labelit=T,legend=T,rainbow=T,
xlim=c(1,max),ylim=c(0,rich),type="p",xlab="sites",
ylab="species richness",...)
``` |

### Arguments

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

`y` |
Environmental data frame. |

`factor` |
Variable of the environmental data frame that defines subsets to calculate species accumulation curves for. |

`level` |
Level of the variable to create the subset to calculate species accumulation curves. |

`scale` |
Continuous variable of the environmental data frame that defines the variable that scales the horizontal axis of the species accumulation curves. |

`method` |
Method of calculating the species accumulation curve (as in function |

`permutations` |
Number of permutations to calculate the species accumulation curve (as in function |

`conditioned` |
Estimation of standard deviation is conditional on the empirical dataset for the exact SAC (as in function |

`gamma` |
Method for estimating the total extrapolated number of species in the survey area (as in |

`addit` |
Add species accumulation curve to an existing graph. |

`xr` |
Result from |

`col` |
Colour for drawing lines of the species accumulation curve (as in function |

`labels` |
Labels to plot at left and right of the species accumulation curves. |

`ci` |
Multiplier used to get confidence intervals from standard deviatione (as in function |

`pch` |
Symbol used for drawing the species accumulation curve (as in function |

`type` |
Type of plot (as in function |

`cex` |
Character expansion factor (as in function |

`xlim` |
Limits for the horizontal axis. |

`ylim` |
Limits for the vertical axis. |

`xlab` |
Label for the horizontal axis. |

`ylab` |
Label for the vertical axis. |

`plotit` |
Plot the results. |

`labelit` |
Label the species accumulation curves with the levels of the categorical variable. |

`legend` |
Add the legend (you need to click in the graph where the legend needs to be plotted). |

`rainbow` |
Use rainbow colouring for the different curves. |

`...` |
Other items passed to function |

### Details

These functions provide some alternative methods of obtaining species accumulation results, although function `specaccum`

is called by these functions to calculate the actual species accumulation curve.

Functions `accumresult`

and `accumcomp`

allow to calculate species accumulation curves for subsets of the community and environmental data sets. Function `accumresult`

calculates the species accumulation curve for the specified level of a selected environmental variable. Method `accumcomp`

calculates the species accumulation curve for all levels of a selected environmental variable separatedly. Both methods allow to scale the horizontal axis by multiples of the average of a selected continuous variable from the environmental dataset (hint: add the abundance of each site to the environmental data frame to scale accumulation results by mean abundance).

Functions `accumcomp`

and `accumplot`

provide alternative methods of plotting species accumulation curve results, although function `plot.specaccum`

is called by these functions. When you choose to add a legend, make sure that you click in the graph on the spot where you want to put the legend.

### Value

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

and `plot.specaccum`

.

### Author(s)

Roeland Kindt (World Agroforestry Centre)

### References

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

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

### Examples

1 2 3 4 5 6 7 8 9 10 | ```
library(vegan)
data(dune.env)
data(dune)
dune.env$site.totals <- apply(dune,1,sum)
Accum.1 <- accumresult(dune, y=dune.env, scale='site.totals', method='exact', conditioned=TRUE)
Accum.1
accumplot(Accum.1)
accumcomp(dune, y=dune.env, factor='Management', method='exact', legend=FALSE, conditioned=TRUE)
## CLICK IN THE GRAPH TO INDICATE WHERE THE LEGEND NEEDS TO BE PLACED FOR
## OPTION WHERE LEGEND=TRUE (DEFAULT).
``` |