**Analysis of Species Richness Data: Example**

John R. Sauer and James E. Hines

USGS Pauxent Wildlife Research Center

12100 Beech Forest Road

Laurel, MD

These examples document the use of 3 programs for estimation of species
richness from count data (Hines et al. 1999). Programs and additional
information are available on the internet, at:

http://www.mbr-pwrc.usgs.gov/software/comdyn.html

In addition, this site provides documentation, pdf files of relevant
literature, and metadata for use of these programs with Breeding Bird
Survey data:

http://www.mbr-pwrc.usgs.gov/software/comdyn3.html

**Species Richness Computations**

SPECRICH - Computes \"species richness\" or total number of species from
empirical species abundance distribution data. Program written by J.E.
Hines based on the limiting form of the jackknife estimators as
described by Burnham and Overton (1979).

-   [Program Documentation](../SPECRICH_doc.txt)

-   [Sample Dataset](../SPECRICH_DAT.txt)

-   [Sample Output](../SPECRICH_out.txt)

SPECRICH2 - Estimates the total number of species from species
presence-absence data on multiple sample sites or occasions using the
jackknife estimator for model M(h) from program CAPTURE. (Closed model
capture-recapture analysis: model with heterogeneous capture
probabilities, White et al. 1978)

-   [Program Documentation](../specric2_doc.txt)

-   [Sample Dataset](../specric2_dat.txt)

-   [Sample Output](../specric2_OUT.txt)

**Community Dynamics**

COMDYN was developed to estimate parameters associated with community
dynamics using presence/absence data from 2 locations or time periods.
The basic estimator for species richness underlying all estimators is
the jackknife estimator proposed by Burnham and Overton (1979).
Application of this estimator to species richness estimation is
described and justified by Boulinier et al. (1998). The estimators for
community-dynamic parameters and their variances are presented by
Nichols et al. (1998a,b).

COMDYN4 - Compares 2 routes/years from user input

-   [Program Documentation](../comdyn4_doc.txt)

-   [Sample Dataset](../comdyn4_dat.txt)

-   [Sample Output](../comdyn4_out.txt)

COMDYN3 - Internet-oriented Program designed for analysis of Breeding
Bird Survey data.Compares 2 routes/years from BBS allowing the data to
be subset by individual species or allowing data for eastern forest bird
species to be subset by area-sensitivity, based on Robbins et al. (1989)

-   [Link to Internet Program and
    Documentation](http://www.mbr-pwrc.usgs.gov/software/comdyn3.html)

Literature Cited

Boulinier, T, J. D. Nichols, J. R. Sauer, J. E. Hines, and K. H.
Pollock. 1998b. Estimating species richness to make inference in
community ecology: The importance of heterogeneity in species
detectability as shown from capture-recapture analyses of North American
Breeding Bird Survey Data. Ecology 79:1018-1028.

Burnham, K. P. and W. S. Overton. 1979. Robust estimation of population
size when capture probabilities vary among animals. Ecology 60:927-936.

Hines, J.E., T. Boulinier, J.D. Nichols, J.R. Sauer, and K.H. Pollock.
1999. COMDYN: software to study the dynamics of animal communities using
a capture-recapture approach. Bird Study 46 (suppl.):S209-217.

Nichols, J. D., T. Boulinier, J. E. Hines, K. H. Pollock, and J. R.
Sauer. 1998a. Estimating rates of local species extinction,
colonization, and turnover in animal communities. Ecological
Applications 8:1213-1225.

Nichols, J. D., T. Boulinier, J. E. Hines, K. H. Pollock, and J. R.
Sauer. 1998b. Inference methods for spatial variation in species
richness and community composition when not all species are detected.
Conservation Biology 12:1390-1398.

Robbins, C. S. , D. K. Dawson and B. A. Dowell. 1989. Habitat area
requirements of breeding forest birds of the middle Atlantic states.
Wildlife Monographs 103.

White, G.C., K.P. Burnham, D.L. Otis, and D.R. Anderson. 1978.

User\'s Manual for Program CAPTURE, Utah State Univ. Press,

Logan, Utah.