# Estimation of the number of shared species between two communities/assemblages

### Description

`ChaoShared`

: Estimation of shared species richness between two communities/assemblages based on
three types of data: Type (1) abundance data (datatype="abundance"), Type (2) incidence-frequency
data (datatype="incidence_freq"), and Type (2B) incidence-raw data (datatype="incidence

_raw"); see `SpadeR-package`

details for data input formats.

### Usage

1 2 | ```
ChaoShared(data, datatype = c("abundance", "incidence_freq", "incidence_raw"),
units, se = TRUE, nboot = 200, conf = 0.95)
``` |

### Arguments

`data` |
a matrix/data.frame of species abundances/incidences. |

`datatype` |
type of input data, "abundance", "incidence_freq" or "incidence_raw". |

`units` |
number of sampling units in each community. For |

`se` |
a logical variable to calculate the bootstrap standard error and the associated confidence interval. |

`nboot` |
an integer specifying the number of bootstrap replications. |

`conf` |
a positive number |

### Value

a list of two objects:

`$Basic_data_information`

for summarizing data information.

`$Estimation_results`

for showing a table of various shared richess estimates, standard errors, and the associated confidence intervals.

### References

Chao, A., Hwang, W.-H., Chen, Y.-C. and Kuo. C.-Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica, 10, 227-246.

Pan, H.-Y., Chao, A. and Foissner, W. (2009). A non-parametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics, 14, 452-468.

### Examples

1 2 3 4 5 6 7 | ```
data(ChaoSharedData)
# Type (1) abundance data
ChaoShared(ChaoSharedData$Abu,"abundance",se=TRUE,nboot=200,conf=0.95)
# Type (2) incidence-frequency data
ChaoShared(ChaoSharedData$Inci,"incidence_freq",se=TRUE,nboot=200,conf=0.95)
# Type (2B) incidence-raw data
ChaoShared(ChaoSharedData$Inci_raw,"incidence_raw",units=c(16,17),se=TRUE,nboot=200,conf=0.95)
``` |