Avian Diet Database
This repository is the temporary home for the Avian Diet Database being built by the Hurlbert Lab at the University of North Carolina.
The goal is to organize all available information (from published studies, gray literature, etc) on the diets of North American birds in its rawest form possible with the idea that this may be a resource for a broad range of ecological questions.
These data are automatically incorporated into the Global Biotic Interactions (GloBI) database. See http://www.globalbioticinteractions.org for more details.
Finding Diet Data
We are focusing our search for diet data in the published literature. References related to avian diets have been scraped from individual species accounts on the Birds of North America website, and are provided in the file 'NA_avian_diet_refs.txt'. For each species, look up the listed references to see if they contain raw diet data summaries. If you were able to look up the reference, put a 'y' in the 'checked' column. If the reference was unavailable (couldn't access it online, not in the library) put a 'n'. For those that you checked, indicate (y/n) whether it contained diet data in the 'useable_data' column.
NOTE: Place pdfs of all papers you find with usable data in the following folder on the HurlbertLab drive: HurlbertLab > Databases > DietDatabase > Papers with data. The file should be saved with the last name of the author(s) and the year. For example, "Beaver and Baldwin 1975.pdf" or "Hurlbert et al 2007.pdf".
After you have examined all of the references listed in this table for a given species, you will perform a literature search to see if any additional papers have been published on the diet of this species since the Birds of North America species account was published or last revised (the year in the "revised" column).
Web of Science search
Go to Web of Science and in the Topic search box enter:
"[common name]" AND (diet OR foraging OR food)
replacing [common name] with the actual common name of the species you are searching.
Click on +Add Another Field, and select Year Published. Search all years since the last revised date for that species as listed in the 'NA_avian_diet_refs' table.
Look up the papers in the search results, and be sure to add any that contain useful data to the NA_avian_diet_refs.txt table.
Data Entry Details
When you've found a study with quantitative diet data, open the file 'AvianDietDatabase_template.txt' in Excel and re-save it, replacing the word 'template' with the study author and year, e.g. 'AvianDietDatabase_Beaver_and_Baldwin_1975.txt'. Then proceed to enter as much of the information described below as you can ascertain from the study.
To maximize the utility of the data, we need to record many types of information describing the what, when, where, and how of its collection, and so our database has many fields. In the table below we explain what exactly is characterized in each of these fields, and how data should be entered. Further instructions about how to enter data in the database are provided here.
|Common_Name||The common name of the species whose diet is being characterized, following the most recent Clements / eBird checklist. Make sure that this is the currently accepted name by checking http://help.ebird.org/customer/portal/kb_article_attachments/35388/original.xls?1407441617 and http://avibase.bsc-eoc.org/. Names from older papers are potentially out of date and will need to be fixed.|
|Scientific_Name||Genus and species of the species whose diet is being characterized. For North American birds we will generally follow the most recent Clements / eBird checklist. Make sure that this is the currently accepted name by checking http://help.ebird.org/customer/portal/kb_article_attachments/35388/original.xls?1407441617 and http://avibase.bsc-eoc.org/. Names from older papers are potentially out of date and will need to be fixed.|
|Family||Family of the species whose diet is being characterized.|
|Taxonomy||The taxonomic authority for the scientific name. For example, eBird Clements checklist v2016.|
|Longitude_dd||Longitude of the study, if provided, in decimal degrees. NOTE: Most studies that provide lat-long info will do so by providing it in degree-minutes-seconds, e.g. 89W 30' 15", so you will have to convert such values to decimal degrees. Do this by adding up the degrees, the minutes/60, and the seconds/3600. E.g., 89 + 30/60 + 15/3600. Lastly, all longitudes west of the prime meridian (e.g. in North America) are NEGATIVE, so be sure to put a minus sign in front!|
|Latitude_dd||Latitude of the study, if provided, in decimal degrees. Latitudes south of the equator are NEGATIVE.|
|Altitude_min_m||Minimum altitude of the study in meters if a range was provided. If altitude is given in anything other than meters, don't forget to convert first!|
|Altitude_mean_m||Altitude of the study in meters if a single value was provided. If altitude is given in anything other than meters, don't forget to convert first!|
|Altitude_max_m||Maximum altitude of the study in meters if a range was provided. If altitude is given in anything other than meters, don't forget to convert first!|
|Location_Region||Location of the study based on national or subnational place name (e.g., Florida, or Jamaica). If the study spans multiple regions they can be listed separated by semi-colons (e.g. "Florida; Alabama; Georgia").|
|Location_Specific||Location of the study using the most specific placename provided in the study (e.g. Hubbard Brook Experimental Forest, or Huachuca Mountains, or Dare County).|
|Habitat_type||List one or more of the following habitat designations describing the habitat in which the study was conducted. If listing multiple habitat types, use a ";" to separate them. +forest +deciduous forest +coniferous forest +woodland +scrubland +grassland +desert +wetland +agriculture +urban +tundra +mudflats E.g. "deciduous forest; woodland"|
|Observation_Month_Begin||The month in which diet data were first collected, using numbers 1-12.|
|Observation_Year_Begin||The year in which diet data were first collected in the study.|
|Observation_Month_End||The month in which diet data were last collected, using numbers 1-12.|
|Observation_Year_End||The year in which diet data were last collected in the study.|
|Observation_Season||The season(s) in which diet data were last collected. Possible values include spring, summer, fall, winter, or multiple.|
|Prey_Kingdom||Kingdom to which the prey item belongs (e.g. Plantae, Animalia).|
|Prey_Phylum||Phylum to which the prey item belongs (e.g. Arthropoda).|
|Prey_Class||Class to which the prey item belongs (e.g. Insecta).|
|Prey_Order||Order to which the prey item belongs (e.g. Lepidoptera).|
|Prey_Suborder||Suborder to which the prey item belongs. This field will most frequently be used when older studies report prey orders "Homoptera", "Hemiptera", and "Heteroptera", which now all fall under the Order Hemiptera. Thus, a report of "Homoptera" should be classified as Order Hemiptera, Suborder Homoptera. An older (pre-2000s) report of "Hemiptera" should be classified as Order Hemiptera, Suborder Heteroptera.|
|Prey_Family||Family to which the prey item belongs (e.g. Formicidae).|
|Prey_Genus||Genus to which the prey item belongs. If the prey was identified to species, this field can be left blank and reported under Prey_Scientific_Name.|
|Prey_Scientific_Name||The full scientific name, genus and species, to which the prey item belongs.|
|Unidentified||If "NO", then the diet fraction reported represents the fraction made up by all members of that lowest level of taxonomic classification reported. If "YES", then the diet fraction reported represents the fraction made up by those members of that lowest level of taxonomic classification reported that were not identified to lower levels. For example, let's say some diet items are identified to various families within Coleoptera, while some diet items are listed as "Unidentified Coleoptera" with the family unknown. In this case, we would have separate lines for the families "Tenebrionidae" and "Carabidae" for which Unidentified would be "NO", but we might also have a line that identifies only down to Order Coleoptera for which Unidentified would be "YES" because the value in this row does not represent the fraction of the diet made up of all Coleoptera, only the Coleoptera that were not assigned to other groups. Use this field rather than ever entering "Unidentified" or "Unknown" in any of the prey taxonomic rank fields.|
|Prey_Name_ITIS_ID||The Integrated Taxonomic Information Service (ITIS) taxon ID associated with the prey item. This field should be left blank and will be populated by an R script automatically.|
|Prey_Name_Status||Taxonomic status of the prey name. "Verified" indicates the name matched a valid ITIS ID. "Unverified" means the name did not match a valid ITIS ID and needs to be investigated further. "Accepted" means the name did not match a valid ITIS ID, but investigation revealed that it reflects an accepted taxonomic entity not in ITIS.|
|Prey_Stage||The lifestage of the identified prey item (e.g., 'adult', 'egg', 'juvenile', 'larva', 'nymph', 'pupa', 'teneral'). In general, you only need to worry about this column if the information is explicitly provided in the data source. BUT NOTE: Always specify 'adult' or 'larva' for the Prey_Order "Lepidoptera" if you can figure it out.|
|Prey_Part||The part of the prey species represented in the diet if only a part was (likely) consumed. Especially for plant-based diet items, e.g., 'bark', 'bud', 'dung', 'egg', 'feces', 'flower', 'fruit','gall', 'oogonium', 'pollen', 'root', 'sap', 'seed','spore', 'statoblasts', 'vegetation'.|
|Prey_Common_Name||Common name of the prey item if provided.|
|Fraction_Diet||Fraction of the bird's diet made up by this prey item. Convert all %s to fractions between 0 and 1.|
|Diet_Type||4 possible values. Wt_or_Vol: Fraction of the diet as measured by weight or volume. E.g., all beetles in the stomach contents were weighed, and this value was divided by the mass of all stomach contents. Items: Fraction of the diet as measured by a count of the number of prey items. E.g., the number of beetles in the stomach contents were counted, and this value was divided by the total number of unique prey items in the stomach contents. Occurrence: Fraction of the birds examined that contained at least one individual of this prey type. Unspecified: Fraction of the diet of the prey item based on a methodology unspecified by the authors.|
|Item_Sample_Size||Total number of prey items identified in the diet sample.|
|Bird_Sample_Size||Total number of individuals of the focal bird species used to characterize diet.|
|Sites||Number of study sites over which individuals were used to characterize the diet.|
|Study_Type||The way that diet data were collected. Options include: emetic, fecal contents, stomach contents, esophagus contents, crop contents, pellet contents, behavioral observation, nest debris, prey remains.|
|Notes||Any useful information about the nature of the study or the diet information that does not fit in the previous fields.|
|Entered_By||Initials of the person entering the data.|
|Source||The complete citation of the study from which the diet information comes.|
We use a version control system called Git to manage so that we can easily go back to previous states, it's automatically backed up, and many people can access it and add records simultaneously from different computers.
See this page for instructions on how to use Git to manage the Avian Diet Database.
See this page for instructions on cleaning newly entered data.
dbSummary() function to get summary statistics for the diet database as a whole.
> dbSummary() $numRecords  29548 $numSpecies  432 $numStudies  539 $recordsPerSpecies Common_Name n 1 Abert's Towhee 5 2 Acadian Flycatcher 32 3 Acorn Woodpecker 70 4 African Pygmy-Goose 10 5 Alder/Willow Flycatcher (Traill's Flycatcher) 88 6 American Black Duck 43 7 American Crow 211 8 American Goldfinch 17 ... $speciesPerFamily Order Family SpeciesWithData WithoutData 1 Accipitriformes Accipitridae 25 5 2 Accipitriformes Cathartidae 3 1 3 Accipitriformes Pandionidae 1 0 4 Anseriformes Anatidae 100 4 5 Anseriformes Anhimidae 1 0 6 Anseriformes Anseranatidae 1 0 7 Caprimulgiformes Apodidae 2 2 8 Caprimulgiformes Caprimulgidae 4 4 9 Caprimulgiformes Trochilidae 3 11 ...
speciesSummary() function will summarize all of the information available for a given bird species.
> speciesSummary("Black-throated Blue Warbler") $numStudies  3 $Studies  "King, F. H. 1883. Economic relations of Wisconsin birds. Geology of Wisconsin 441-610."  "Robinson, S. K. and R. T. Holmes. 1982. Foraging behavior of forest birds: the relationship among search tactics, diet, and habitat structure. Ecology 63:1918-1931."  "Robinson, S. K. and R. T. Holmes. 1982. Foraging behavior of forest birds: the relationships among search tactics, diet, and habitat structure. Ecology 63:1918-1931." $numRecords  17 $recordsPerYear Observation_Year_Begin n 1 1875 3 2 1974 10 3 1976 4 $recordsPerRegion Location_Region n 1 New Hampshire 9 2 United States 5 3 Wisconsin 3 $recordsPerType Diet_Type n 1 Items 14 2 Occurrence 3 $analysesPerDietType Diet_Type n 1 Items 3 2 Occurrence 1 $preySummary Diet_Type Taxon Frac_Diet 1 Items Lepidoptera larvae 0.26900000 2 Items Coleoptera 0.16666667 3 Items coleoptera adult 0.16666667 4 Items Lepidoptera Larvae 0.09200000 5 Items Lepidoptera Larval 0.09200000 6 Items Lepidoptera adult 0.04600000 7 Items Diptera 0.04600000 8 Items Diptera adult 0.04000000 9 Items Homoptera 0.01733333 10 Items Homoptera adult 0.01733333 11 Items Hymenoptera 0.01733333 12 Items Hymenoptera adult 0.01733333 13 Items Araneae 0.01233333 14 Occurrence Coleoptera 0.83333333 15 Occurrence Hymenoptera 0.16666667 16 Occurrence Lepidoptera 0.16666667