ChaoShared: Estimation of the number of shared species between two...

Description Usage Arguments Value References Examples

View source: R/spader.R

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

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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 datatype = "incidence_raw", users must specify the number of sampling units taken from each community. This argument is not needed for "abundance" and "incidence_freq" data.

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 1 specifying the level of confidence interval.

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

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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)

Example output

(1) BASIC DATA INFORMATION:

    Sample size in Community 1                      n1  =  85867 
    Sample size in Community 2                      n2  =  59646 
    Number of observed species in Community 1       D1  =  155 
    Number of observed species in Community 2       D2  =  140 
    Number of observed shared species               D12 =  111 
    Bootstrap replications for s.e. estimate               200 

    "Entire" Shared Species Group: 
         Some statistics: 
         --------------------------------------------------------------------------- 
         f[11] = 4 ;  f[1+] = 10 ; f[+1] = 15 ;  f[2+] = 2 ;  f[+2] = 7 ; f[22] = 0 
         --------------------------------------------------------------------------- 

    "Rare" Shared Species Group: (Both frequencies can only up to 10) 
         Some statistics: 
         ------------------------------------------------------------------- 
         f[1+]_rare = 8 ; f[+1]_rare = 9 ;  f[2+]_rare = 1 ;  f[+2]_rare = 4 
         ------------------------------------------------------------------- 
    Number of observed individuals in Community 1     n1_rare   =  3358 
    Number of observed individuals in Community 2     n2_rare   =  558 
    Number of observed shared species                 D12_rare  =  21 
    Estimated sample coverage                         C12_rare  =  0.86 
    Estimated CCVs                                    CCV_1     =  0.733 
                                                      CCV_2     =  1.007 
                                                      CCV_12    =  0.457 


(2) ESTIMATION RESULTS OF THE NUMBER OF SHARED SPECIES:

                              Estimate   s.e. 95%Lower 95%Upper
    Homogeneous                114.429  6.682  110.524  147.459
    Heterogeneous(ACE-shared)  133.921 18.155  116.378  199.717
    Chao1-shared               142.125 18.364  121.329  201.090
    Chao1-shared-bc            142.125 18.364  121.329  201.090


(3) DESCRIPTION OF MODELS FOR ESTIMATING SHARED SPECIES RICHNESS:

Homogeneous: This model assumes that the shared species in each community have the same discovery probabilities; see the Eq. (3.11a) of Chao et al. (2000).

Heterogeneous (ACE-shared): This model allows for heterogeneous discovery probabilities among shared species; see Eq. (3.11b) of Chao et al. (2000). It is an extension of the ACE estimator to two communities. It is replaced by Chao1-shared when the estimated sample coverage for rare shared species group (C12_rare in the output) is zero.

Chao1-shared: An extension of the Chao1 estimator to estimate shared species richness between two communities. It provides a lower bound of shared species richness. See Eq. (3.6) of Pan et al. (2009). It is replaced by Chao1-shared-bc for the case f[2+]=0 or f[+2]=0.
   
Chao1-shared-bc: A bias-corrected form of Chao1-shared estimator; See Pan et al. (2009).
	
(1) BASIC DATA INFORMATION:

    Number of sampling units in Community 1               T1  =  16 
    Number of sampling units in Community 2               T2  =  17 
    Number of total incidences in Community 1             U1  =  1958 
    Number of total incidences in Community 2             U2  =  2215 
    Number of observed species in Community 1             D1  =  223 
    Number of observed species in Community 2             D2  =  223 
    Number of observed shared species in two communities  D12 =  196 
    Bootstrap replications for s.e. estimate                     200 

     Some statistics: 
         -------------------------------------------------------------------------- 
         Q[11] = 5 ;  Q[1+] = 16 ; Q[+1] = 11 ;  Q[2+] = 16 ;  Q[+2] = 6 ; Q[22] = 2 
         -------------------------------------------------------------------------- 


(2) ESTIMATION RESULTS OF THE NUMBER OF SHARED SPECIES:

                    Estimate   s.e. 95%Lower 95%Upper
    Chao2-shared     215.748 12.000  202.581  255.253
    Chao2-shared-bc  211.483  9.245  201.246  241.697


(3) DESCRIPTION OF MODELS FOR ESTIMATING SHARED SPECIES RICHNESS:

Chao2-shared: An extension of the Chao2 estimator to estimate shared species richness between two communities. It provides a lower bound of shared species richness. See Pan et al. (2009). It is replaced by Chao2-shared-bc for the case Q[2+]=0 or Q[+2]=0.

Chao2-shared-bc: A bias-corrected form of Chao2-shared. See Pan et al. (2009).
	
(1) BASIC DATA INFORMATION:

    Number of sampling units in Community 1               T1  =  16 
    Number of sampling units in Community 2               T2  =  17 
    Number of total incidences in Community 1             U1  =  1958 
    Number of total incidences in Community 2             U2  =  2215 
    Number of observed species in Community 1             D1  =  223 
    Number of observed species in Community 2             D2  =  223 
    Number of observed shared species in two communities  D12 =  196 
    Bootstrap replications for s.e. estimate                     200 

     Some statistics: 
         -------------------------------------------------------------------------- 
         Q[11] = 5 ;  Q[1+] = 16 ; Q[+1] = 11 ;  Q[2+] = 16 ;  Q[+2] = 6 ; Q[22] = 2 
         -------------------------------------------------------------------------- 


(2) ESTIMATION RESULTS OF THE NUMBER OF SHARED SPECIES:

                    Estimate   s.e. 95%Lower 95%Upper
    Chao2-shared     215.748 12.000  202.581  255.253
    Chao2-shared-bc  211.483  9.245  201.246  241.697


(3) DESCRIPTION OF MODELS FOR ESTIMATING SHARED SPECIES RICHNESS:

Chao2-shared: An extension of the Chao2 estimator to estimate shared species richness between two communities. It provides a lower bound of shared species richness. See Pan et al. (2009). It is replaced by Chao2-shared-bc for the case Q[2+]=0 or Q[+2]=0.

Chao2-shared-bc: A bias-corrected form of Chao2-shared. See Pan et al. (2009).
	

SpadeR documentation built on May 30, 2017, 8:12 a.m.