ComDyn - Community Dynamics Analysis with BBS data

Estimation of Bird Community Dynamics from Breeding Bird Survey Data

Using Program COMDYN

Background

The BBS provides a unique source of information about bird communities, and many investigators use BBS data to evaluate change in species richness over time and space (e.g., Boulinier 1998a).  Unfortunately, the naive estimate of total number of observed species on a BBS routes is biased, as all observers have some chance of missing species during the counts and this chance is well known to differ among observers and routes (Boulinier et al. 1998b).  This is a very real problem, and investigators who use simple counts of species on BBS routes in ecological studies must recognize that their estimates of species richness and change in richness are flawed and could be subject to criticism or rebuttal.

Luckily, estimators of species richness have been developed to estimate detection rates of species, and to accommodate variation in detection rates among species and sites (e.g.  Burnham and Overton 1979).  Nichols et al. (1998a,b) have developed a series of estimators for change in communities that incorporate the possibility of variation in detection rates among species.  Program COMDYN (Hines et al. 1999) implements these estimators of change over time and space for the North American Breeding Bird Survey.  Detailed descriptions of the estimators in program COMDYN can be found in Nichols et al. (1998a, 1998b). These papers, along with papers describing Shrother examples and applications of species richness estimation methods, are available either from this website (as pdf files) or from the authors.

Using Program COMDYN

To use the program, enter the state/province and routes to be compared, and the years to include in the comparison. Note: routes are indexed by numbers. To obtain the names of routes, consult either the Analysis website or the Electronic National Atlas. The program also allows you to choose whether "occurrence" is summarized at the scale of individual stops (Analyze stops individually) or over groups of 10 stops (Analyze stops in groups of 10). For bootstrap confidence interval estimation, users can (optionally) choose number of replicates and a random number seed. Then, choose "Select species" to initiate the program and generate a list of species found on the routes.

The program will respond with a list of species found on the routes, and the user must choose the appropriate species for the analysis. The default is that all species are included (all are "checked"). You can either select (or unselect) species by clicking on the buttons, or by selecting from the selection bars under the species list. Note that "Select no species" and "Select all species" are options on the list. Then, select "Compute estimates" to run the program. Results are presented on a new page, and definitions of parameters and estimates are provided below the numeric outputs.

LITERATURE CITED

Boulinier, T, J. D. Nichols, J. E. Hines, J. R. Sauer, C. H. Flather, and K. H. Pollock. 1998a. Higher temporal variability of forest bird communities in fragmented landscapes. Proc. Nat. Acad. Sci. 95:7497-7501.Download PDF

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.Download PDF

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

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.View Abstract

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.Download PDF

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.View Abstract

ADDITIONAL REFERENCES ON COMMUNITY DYNAMICS ESTIMATION

Cam, E., J. R. Sauer, J. D. Nichols, J. E. Hines, and C. H. Flather. 2000. Geographic analysis of species richness and community attributes of forest birds from survey data in the mid-atlantic integrated assessment region Environmental Monitoring and Assessment 63:81-94.Download PDF

Cam, E., J. D. Nichols, J. E. Hines, and J. R. Sauer. 2000. Inference about nested subsets structure when not all species are detected. Oikos 91: 428-434.

Nichols, J. D., J. R. Sauer, J. E. Hines, and T. Boulinier, and K. H. Pollock. 2001. Estimation of Species Richness and Parameters Reflecting Community Dynamics Using Data from Ecological Monitoring Programs. Pages 181- 187 in Conservation of biological diversity: A key to the restoration of the Chesapeake Bay Ecosystem and Beyond. G. D. Therres, Ed. Maryland Department of Natural Resources, Annapolis, MD.

Boulinier, T. Nichols, J. D., J. E. Hines, J. R. Sauer, C. H. Flather, and K. H. Pollock. 2001. Forest fragmentation and bird community dynamics: inference at regional scales. Ecology 82:1159-1169.Download PDF

Sauer, J. R., J. D. Nichols, J. E. Hines, T. Boulinier, C. H. Flather, and W. L. Kendall. 2001. Regional patterns in proportion of bird species detected in the North American Breeding Bird Survey Pages 293-296 In R. Field, R. J. Warren, H. Okarma, and P. R. Sievert, editors. Wildlife, land, and people: priorities for the 21^st century. Proceedings of the. 2^nd. International Wildlife Congress. The Wildlife Society, Bethesda, MD, USA.

Cam, E., J. D. Nichols, J. E. Hines, J. R. Sauer, R. Alpizar-Jara, and C. H. Flather. 2002. Disentangling sampling and ecological explanations underlying species-area relationships. Ecology 83:1118-1130.Download PDF

Cam, E., J. D. Nichols, , J. R. Sauer J. E. Hines. 2002. On the estimation of species richness based on the accumulation of previously unrecorded species. Ecography 25:102-108.View Abstract

 

Metadata:

• Identification_Information
• Data_Quality_Information
• Distribution_Information
• Metadata_Reference_Information

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Identification_Information:

Citation:

Citation_Information:

Originator:James E. Hines

Publication_Date:2003

Title:

COMDYN

Geospatial_Data_Presentation_Form:software

Publication_Information:

Publication_Place:Laurel, Maryland

Publisher:U.S. Geological Survey, Biological Resources Division, Patuxent Wildlife Research Center

Description:

Abstract:

Estimators of species richness have been developed to estimate detection rates of species, and to accommodate of variation in detection rates among species and sites (e.g.  Burnham and Overton 1979).  Nichols et al. (1998a,b) have developed a series of estimators for change in communities that incorporate the possibility of variation in detection rates among species.  Program COMDYN (Hines et al. 1999) implements these estimators of change over time and space for the North American Breeding Bird Survey.  Detailed descriptions of the estimators in program COMDYN can be found in Nichols et al. (1998a, 1998b).

Purpose:

COMDYN implements estimators for change in community dynamics from Breeding Bird Survey (BBS) data.

Supplemental_Information:

The information for this metadata was taken from <a href=/software/doc/estimation_of_bird_community_dyn.html>/software/doc/estimation_of_bird_community_dyn.html</a>.

Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date:Unknown

Currentness_Reference:

publication date

Status:

Progress:Complete

Maintenance_and_Update_Frequency:Unknown

Keywords:

Theme:

Theme_Keyword_Thesaurus:none

Theme_Keyword:community dynamics estimates

Theme_Keyword:recovery species richness estimates

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus:none

Taxonomic_Keywords:birds

Taxonomic_Classification:

Taxon_Rank_Name:Kingdom

Taxon_Rank_Value:Animalia

Taxonomic_Classification:

Taxon_Rank_Name:Phylum

Taxon_Rank_Value:Chordata

Taxonomic_Classification:

Taxon_Rank_Name:Class

Taxon_Rank_Value:Aves

Access_Constraints:none

Use_Constraints:

none

Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person:James E. Hines

Contact_Organization:U.S. Geological Survey, Biological Resources Division

Contact_Address:

Address_Type:mailing address

Address:12100 Beech Forest Rd. #201

City:Laurel

State_or_Province:Maryland

Postal_Code:20708-4017

Contact_Voice_Telephone:301 497-5661

Contact_Electronic_Mail_Address:JHines@usgs.gov

Data_Set_Credit:

We thank the many volunteers that collect BBS data.

Cross_Reference:

Citation_Information:Hines, J.E., T. Boulinier, J.D. Nichols, J.R. Sauer, and K.H. Pollock. 1999. 

Originator:Hines, J.E., T. Boulinier, J.D. Nichols, J.R. Sauer, and K.H. Pollock.

Publication_Date:1999

Title:

COMDYN: software to study the dynamics of animal communities using a capture-recapture approach. 

Geospatial_Data_Presentation_Form:Published Journal Article

Series_Information:

Series_Name:.Bird Study 

Issue_Identification:46 (suppl.):S209-217.

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Data_Quality_Information:

Logical_Consistency_Report:

not applicable

Completeness_Report:

not applicable

Lineage:

Process_Step:

Process_Description:

The program allows for comparisons of species richness of bird populations over space and time

Process_Date:Unknown

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Distribution_Information:

Distributor:

Contact_Information:

Contact_Person_Primary:

Contact_Person:James E. Hines

Contact_Organization:U.S. Geological Survey, Biological Resources Division

Contact_Address:

Address_Type:mailing address

Address:12100 Beech Forest Rd.

City:Laurel

State_or_Province:Maryland

Postal_Code:20708-4017

Contact_Voice_Telephone:301 497-5661

Contact_Electronic_Mail_Address:JHines@usgs.gov

Distribution_Liability:

Although these data have been processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from a U.S.. Geological Survey server, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be paid to the contents of the metadata file associated with these data. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and/or contained herein.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name:ZIP

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name:<a href="/software">/software</a>

Fees:None if available online.

Technical_Prerequisites:

Program COMDYN is run interactively on a SUN workstation at the Patuxent Wildlife Research Center, using fortran programs and PERL scripts.  Occasionally, a route will be selected that does not contain data for a year of interest.  In that case, zeros will be output by the program.

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Metadata_Reference_Information:

Metadata_Date:20020329

Metadata_Future_Review_Date:20030329

Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person:Jane E. Fallon

Contact_Organization:Patuxent Wildlife Research Center

Contact_Position:Metadata specialist

Contact_Address:

Address_Type:mailing and physical address

Address:12100 Beech Forest Rd

City:Laurel

State_or_Province:Maryland

Postal_Code:20708

Contact_Voice_Telephone:301 497-5664

Contact_Facsimile_Telephone:301-497-5556.

Contact_Electronic_Mail_Address:  JEFallon@usgs.gov

Metadata_Standard_Name:FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version:FGDC-STD-001.1-1999

Metadata_Access_Constraints:none

Metadata_Use_Constraints:

none

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Route,Year Selection Options:

Choose the state for the 1st sample: ==== select === Alabama Alaska Alberta Arizona Arkansas British Columbia California Colorado Connecticut Delaware Florida Georgia Idaho Illinois Indiana Iowa Kansas Kentucky Louisiana Mackenzie, Northwest Territories Maine Manitoba Maryland Massachusetts Mexico Michigan Minnesota Mississippi Missouri Montana Nebraska Nevada New Brunswick Newfoundland New Hampshire New Jersey New Mexico New York North Carolina North Dakota Nova Scotia Ohio Oklahoma Ontario Oregon Pennsylvania Prince Edward Island Quebec Rhode Island Saskatchewan South Carolina South Dakota Tennessee Texas Utah Vermont Virginia Washington West Virginia Wisconsin Wyoming Yukon Antarctica	Choose the state for the 2nd sample: ==== select === Alabama Alaska Alberta Arizona Arkansas British Columbia California Colorado Connecticut Delaware Florida Georgia Idaho Illinois Indiana Iowa Kansas Kentucky Louisiana Mackenzie, Northwest Territories Maine Manitoba Maryland Massachusetts Mexico Michigan Minnesota Mississippi Missouri Montana Nebraska Nevada New Brunswick Newfoundland New Hampshire New Jersey New Mexico New York North Carolina North Dakota Nova Scotia Ohio Oklahoma Ontario Oregon Pennsylvania Prince Edward Island Quebec Rhode Island Saskatchewan South Carolina South Dakota Tennessee Texas Utah Vermont Virginia Washington West Virginia Wisconsin Wyoming Yukon Antarctica
route for 1st sample:002 HILLSBORO	route for 2nd sample:002 HILLSBORO
year for 1st sample:	year for 2nd sample:

number of iterations for the bootstrap estimator:
Enter a seed number: (enter 0 for a random seed)

Analyze stops individually
Analyze stops in groups of 10

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Select species