ChaoShared: Estimation of the number of shared species between two...
In SpadeR: Species-Richness Prediction and Diversity Estimation with R
Description
Usage
Arguments
Value
References
Examples
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 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.
$Estimation_results for showing a table of various shared richess estimates, standard errors, and the associated confidence intervals.
References
Chao, A., Hwang, W.-H., Chen, Y.-C. and Kuo. C.-Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica, 10, 227-246.
Pan, H.-Y., Chao, A. and Foissner, W. (2009). A non-parametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics, 14, 452-468.
Examples
1
2
3
4
5
6
7
data(ChaoSharedData)
# Type (1) abundance data
ChaoShared(ChaoSharedData$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)
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 2, 2019, 3:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value References Examples
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 ≤ 1 specifying the level of confidence interval. |
Value
a list of two objects:
$Basic_data_information for summarizing data information.
$Estimation_results for showing a table of various shared richess estimates, standard errors, and the associated confidence intervals.
References
Chao, A., Hwang, W.-H., Chen, Y.-C. and Kuo. C.-Y. (2000). Estimating the number of shared species in two communities. Statistica Sinica, 10, 227-246.
Pan, H.-Y., Chao, A. and Foissner, W. (2009). A non-parametric lower bound for the number of species shared by multiple communities. Journal of Agricultural, Biological and Environmental Statistics, 14, 452-468.
Examples
1 2 3 4 5 6 7 | data(ChaoSharedData)
# Type (1) abundance data
ChaoShared(ChaoSharedData$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)
|
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).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.