SimilarityPair: Estimation of two-assemblage similarity measures

Description Usage Arguments Value References Examples

View source: R/spader.R

Description

SimilarityPair: Estimation various similarity indices for two assemblages. The richness-based indices include the classic two-community Jaccard and Sorensen indices; the abundance-based indices include the Horn, Morisita-Horn, regional species-overlap, two-community Bray-Curtis and the abundance-based Jaccard and Sorensen indices. Three types of data are supported: 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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SimilarityPair(X, datatype = c("abundance", "incidence_freq",
  "incidence_raw"), units, nboot = 200)

Arguments

X

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.

nboot

an integer specifying the number of replications.

Value

a list of ten objects:

$datatype for showing the specified data types (abundance or incidence).

$info for summarizing data information.

$Empirical_richness for showing the observed values of the richness-based similarity indices include the classic two-community Jaccard and Sorensen indices.

$Empirical_relative for showing the observed values of the equal-weighted similarity indices for comparing species relative abundances including Horn, Morisita-Horn, regional overlap, Chao-Jaccard and Chao-Sorensen abundance (or incidence) measures based on species relative abundances.

$Empirical_WtRelative for showing the observed value of the Horn similarity index for comparing size-weighted species relative abundances based on Shannon entropy under equal-effort sampling.

$Empirical_absolute for showing the observed values of the similarity indices for comparing absolute abundances. These measures include the Shannon-entropy-based measure, Morisita-Horn and the regional overlap measures based on species absolute abundances, as well as the Bray-Curtis index. All measures are valid only under equal-effort sampling.

The corresponding four objects for showing the estimated similarity indices are: $estimated_richness, $estimated_relative, $estimated_WtRelative and $estimated_Absolute.

References

Chao, A., Chazdon, R. L., Colwell, R. K. and Shen, T.-J. (2005). A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecology Letters, 8, 148-159.

Chao, A., and Chiu, C. H. (2016). Bridging the variance and diversity decomposition approaches to beta diversity via similarity and differentiation measures. Methods in Ecology and Evolution, 7, 919-928.

Chao, A., Jost, L., Hsieh, T. C., Ma, K. H., Sherwin, W. B. and Rollins, L. A. (2015). Expected Shannon entropy and Shannon differentiation between subpopulations for neutral genes under the finite island model. Plos One, 10:e0125471.

Chiu, C. H., Jost, L. and Chao, A. (2014). Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers. Ecological Monographs, 84, 21-44.

Examples

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## Not run: 
data(SimilarityPairData)
# Type (1) abundance data 
SimilarityPair(SimilarityPairData$Abu,"abundance",nboot=200)
# Type (2) incidence-frequency data 
SimilarityPair(SimilarityPairData$Inci,"incidence_freq",nboot=200)
# Type (2B) incidence-raw data 
SimilarityPair(SimilarityPairData$Inci_raw,"incidence_raw",units=c(19,17),nboot=200)

## End(Not run)

Example output

(1) BASIC DATA INFORMATION:

    The loaded set includes abundance/incidence data from 2 communities
    and a total of 86 species.

    Samples size in Community 1                            n1  = 557 
    Samples size in Community 2                            n2  = 111 
    Number of observed species in Community 1              D1  = 69 
    Number of observed species in Community 2              D2  = 43 
    Number of observed shared species in two communities   D12 = 26 
    Number of bootstrap replications for s.e. estimate           200 

    Some statistics:
          f[11]= 4 ; f[1+]= 8 ; f[+1]= 10 ; f[2+]= 2 ; f[+2]= 8 ; f[22]= 0 

(2) EMPIRICAL SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity

        C02 (q=0, Sorensen)             0.4643       0.0401       0.3857       0.5429 
        U02 (q=0, Jaccard)              0.3023       0.0303       0.2429       0.3617 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.5502       0.0309       0.4897       0.6108 

        C22 (q=2, Morisita-Horn)        0.7442       0.0369       0.6719       0.8164 
        U22 (q=2, Regional overlap)     0.8533       0.0256       0.8032       0.9035 

        ChaoJaccard-abundance           0.4040       0.0271       0.3509       0.4571 
        ChaoSorensen-abundance          0.5755       0.0297       0.5173       0.6337 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)        0.6002       0.0286       0.5441       0.6563 

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.3894       0.0286       0.3333       0.4455 

        C22 (Morisita-Horn)             0.3039       0.0389       0.2276       0.3802 
        U22 (Regional overlap)          0.4661       0.0465       0.3750       0.5573 

        Bray-Curtis                     0.2425       0.0164       0.2103       0.2747 

(3) ESTIMATED SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity:

        C02 (q=0, Sorensen)             0.4966       0.1579       0.1871       0.8061 
        U02 (q=0, Jaccard)              0.3303       0.1875       -0.0372       0.6978 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.6763       0.0771       0.5253       0.8274 

        C22 (q=2, Morisita-Horn)        0.7868       0.0369       0.7144       0.8591 
        U22 (q=2, Regional overlap)     0.8807       0.0245       0.8327       0.9286 

        ChaoJaccard-abundance           0.4845       0.0806       0.3265       0.6425 
        ChaoSorensen-abundance          0.6527       0.0702       0.5151       0.7903 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)        0.7586       0.0715       0.6184       0.8988 

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.4922       0.0715       0.3520       0.6324 

        C22 (q=2, Morisita-Horn)        0.3114       0.0399       0.2332       0.3896 
        U22 (q=2, Regional overlap)     0.4749       0.0471       0.3825       0.5674 

        Bray-Curtis                     0.2725       0.0410       0.1920       0.3529 

        NOTE: If an estimate is greater than 1, it is replaced by 1.(1) BASIC DATA INFORMATION:

    The loaded set includes abundance/incidence data from 2 communities
    and a total of 200 species.

    Number of sampling units in Community 1                T1  = 217 
    Number of sampling units in Community 2                T2  = 62 
    Number of total incidences in Community 1              U1  = 775 
    Number of total incidences in Community 2              U2  = 455 
    Number of observed species in Community 1              D1  = 117 
    Number of observed species in Community 2              D2  = 103 
    Number of observed shared species in two communities   D12 = 20 
    Number of bootstrap replications for s.e. estimate           200 

    Some Statistics:
          Q[11]= 2 ; Q[1+]= 6 ; Q[+1]= 7 ; Q[2+]= 2 ; Q[+2]= 3 ; Q[22]= 1 

(2) EMPIRICAL SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity

        C02 (q=0, Sorensen)             0.1818       0.0249       0.1330       0.2306 
        U02 (q=0, Jaccard)              0.1000       0.0150       0.0706       0.1294 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.1421       0.0152       0.1124       0.1718 

        C22 (q=2, Morisita-Horn)        0.0931       0.0194       0.0551       0.1311 
        U22 (q=2, Regional overlap)     0.1703       0.0107       0.1494       0.1912 

        ChaoJaccard-abundance           0.1335       0.0163       0.1016       0.1654 
        ChaoSorensen-abundance          0.2356       0.0259       0.1848       0.2864 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)                              

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.1347       0.0162       0.1029       0.1665 

        C22 (Morisita-Horn)             0.0778       0.0153       0.0478       0.1078 
        U22 (Regional overlap)          0.1444       0.0265       0.0923       0.1964 

        Bray-Curtis                     0.0813       0.0101       0.0616       0.1010 

(3) ESTIMATED SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity:

        C02 (q=0, Sorensen)             0.2618       0.0874       0.0905       0.4331 
        U02 (q=0, Jaccard)              0.1506       0.0669       0.0195       0.2817 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.2286       0.0770       0.0776       0.3796 

        C22 (q=2, Morisita-Horn)        0.0994       0.2381       0.0000       0.5661 
        U22 (q=2, Regional overlap)     0.1809       0.0467       0.0894       0.2723 

        ChaoJaccard-abundance           0.1918       0.0415       0.1105       0.2731 
        ChaoSorensen-abundance          0.3218       0.0589       0.2064       0.4372 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)        0.2281       0.0791       0.0731       0.3831 

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.2168       0.0791       0.0618       0.3719 

        C22 (q=2, Morisita-Horn)        0.0835       0.0165       0.0512       0.1157 
        U22 (q=2, Regional overlap)     0.1541       0.0283       0.0987       0.2096 

        Bray-Curtis                     0.1247       0.0346       0.0568       0.1926 

        NOTE: If an estimate is greater than 1, it is replaced by 1.(1) BASIC DATA INFORMATION:

    The loaded set includes abundance/incidence data from 2 communities
    and a total of 262 species.

    Number of sampling units in Community 1                T1  = 19 
    Number of sampling units in Community 2                T2  = 17 
    Number of total incidences in Community 1              U1  = 516 
    Number of total incidences in Community 2              U2  = 380 
    Number of observed species in Community 1              D1  = 216 
    Number of observed species in Community 2              D2  = 130 
    Number of observed shared species in two communities   D12 = 84 
    Number of bootstrap replications for s.e. estimate           200 

    Some Statistics:
          Q[11]= 16 ; Q[1+]= 28 ; Q[+1]= 33 ; Q[2+]= 15 ; Q[+2]= 18 ; Q[22]= 4 

(2) EMPIRICAL SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity

        C02 (q=0, Sorensen)             0.4855       0.0240       0.4385       0.5325 
        U02 (q=0, Jaccard)              0.3206       0.0195       0.2824       0.3588 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.6142       0.0205       0.5741       0.6544 

        C22 (q=2, Morisita-Horn)        0.6551       0.0177       0.6205       0.6897 
        U22 (q=2, Regional overlap)     0.7916       0.0105       0.7710       0.8122 

        ChaoJaccard-abundance           0.5033       0.0234       0.4574       0.5492 
        ChaoSorensen-abundance          0.6696       0.0229       0.6247       0.7145 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)                              

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.6114       0.0204       0.5715       0.6514 

        C22 (Morisita-Horn)             0.6912       0.0327       0.6270       0.7554 
        U22 (Regional overlap)          0.8174       0.0249       0.7686       0.8662 

        Bray-Curtis                     0.4821       0.0203       0.4423       0.5220 

(3) ESTIMATED SIMILARITY INDICES: 

                                       Estimate       s.e.       95%Lower     95%Upper
    (a) Classic richness-based similarity:

        C02 (q=0, Sorensen)             0.5699       0.0964       0.3810       0.7588 
        U02 (q=0, Jaccard)              0.3985       0.1004       0.2017       0.5953 

    (b) Measures for comparing species relative abundances

        C12=U12 (q=1, Horn)             0.7368       0.0480       0.6428       0.8308 

        C22 (q=2, Morisita-Horn)        0.7870       0.0881       0.6143       0.9598 
        U22 (q=2, Regional overlap)     0.8808       0.0631       0.7570       1.0000 

        ChaoJaccard-abundance           0.6534       0.0588       0.5382       0.7686 
        ChaoSorensen-abundance          0.7904       0.0485       0.6953       0.8855 

    (c) Measures for comparing size-weighted species relative abundances

        Horn size-weighted (q=1)        0.7439       0.0461       0.6536       0.8342 

    (d) Measures for comparing species absolute abundances

        C12=U12 (q=1)                   0.7315       0.0461       0.6412       0.8218 

        C22 (q=2, Morisita-Horn)        0.7925       0.0363       0.7214       0.8636 
        U22 (q=2, Regional overlap)     0.8842       0.0251       0.8350       0.9335 

        Bray-Curtis                     0.5440       0.0277       0.4897       0.5982 

        NOTE: If an estimate is greater than 1, it is replaced by 1.

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