README.md
In ahhurlbert/aviandietdb: Avian Diet Database Summary Functions
aviandietdb
aviandietdb provides access to the Avian Diet Database, which contains quantitative diet data for bird species as well as contextual information about where and when those data were collected.
The archived database currently includes 73,075 diet records for 759 bird species. This is a growing database, and while it is currently North American biased, we hope to continue adding avian diet data from around the world.
You can find the development version of the database (which may include more recent records than what is available in the R package but which may still require data cleaning) here.
This R package provides a few simple functions for summarizing and querying the database.
Installation
You can install aviandietdb from GitHub with:
# install.packages("devtools")
devtools::install_github("ahhurlbert/aviandietdb")
Database
Load the library and then the R data file that contains the raw data.
library(aviandietdb)
data(dietdb)
Typing ?dietdb will provide a description of the 42 data fields in this database.
A summary of the total number of records by species, and the total number of species with data by family is provided using dbSummary().
dbSummary()
#> $numRecords
#> [1] 73075
#>
#> $numSpecies
#> [1] 759
#>
#> $numStudies
#> [1] 993
#>
#> $recordsPerSpecies
#> # A tibble: 600 x 3
#> Common_Name Family n
#> <chr> <chr> <int>
#> 1 Abert's Towhee Passerellidae 17
#> 2 Acadian Flycatcher Tyrannidae 150
#> 3 Acorn Woodpecker Picidae 70
#> 4 Adelaide's Warbler Parulidae 34
#> 5 African Pygmy-Goose Anatidae 10
#> 6 Alder/Willow Flycatcher (Traill's Flycatcher) Tyrannidae 87
#> 7 American Avocet Recurvirostridae 8
#> 8 American Black Duck Anatidae 51
#> 9 American Coot Rallidae 198
#> 10 American Crow Corvidae 225
#> # ... with 590 more rows
#>
#> $speciesPerFamily
#> # A tibble: 99 x 5
#> Order Family SpeciesWithData TotalSpeciesABA PercentComplete
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 Accipitriformes Accipitridae 25 35 71
#> 2 Accipitriformes Pandionidae 1 1 100
#> 3 Anseriformes Anatidae 102 116 88
#> 4 Bucerotiformes Upupidae 0 1 0
#> 5 Caprimulgiformes Apodidae 2 10 20
#> 6 Caprimulgiformes Caprimulgidae 5 10 50
#> 7 Caprimulgiformes Trochilidae 16 34 47
#> 8 Cathartiformes Cathartidae 3 4 75
#> 9 Charadriiformes Alcidae 2 23 9
#> 10 Charadriiformes Charadriidae 1 17 6
#> # ... with 89 more rows
Diet_Type
When examining these diet data it is important to understand the different possible ways that investigators may have quantified the importance of different diet items, because these different methods are not necessarily comparable with each other. This means any summaries will be specific to a particular 'Diet_Type'. In this database, the possible values are:
- Items - the fraction of the diet based on the proportion of total diet items examined (e.g. 9 out of 12 prey items examined were ants);
- Wt_or_Vol - the fraction of the diet based on the proportional weight or volume of the prey taxa examined (e.g. ants made up 10% of the diet by mass);
- Occurrence - the proportion of bird specimens (e.g. stomachs, nests, fecal samples) that included at least one of the specified prey taxa (e.g. ants occurred in 90% of stomachs examined); NOTE: this is the one measure that need not sum to 100% across diet items within a given analysis;
- Unspecified - in the event that it is unclear from the Methods section of the study which measure was being used, it is listed as "Unspecified"
Summary functions
For now, we provide just three simple ways to summarize data from the Diet Database.
speciesSummary()
The speciesSummary() function provides a summary of what kinds of data are available for the specified bird species, as well as a quantitative summary at the taxonomic level specified. In the example below, you can see (1) the list of all studies providing quantitative diet data, (2) the total number of diet records, (3) the distribution of those records seasonally, (4) the distribution of those records across years and states/provinces, (5) the distribution of records by the taxonomic level to which prey were identified, (6) the distribution of records by Diet_Type, (7) the total number of diet analyses conducted for each Diet_Type, and (8) a quantitative summary of the diet at the specified taxonomic level averaged across all available studies of a given Diet_Type. If the original data source indicated that specific parts of the prey taxon was consumed (e.g. fruit, seed, vegetation, etc.) then they are listed in the Prey_Part field.
> speciesSummary("Tundra swan", by = "Class")
$Studies
[1] "Owen, M. and C.J. Cadbury. 1975. The ecology and mortality of swans at the Ouse Washes, England. Wildfowl 26:31-42."
[2] "Stewart, R.E. and J.H. Manning. 1958. Distribution and ecology of Whistling Swans in the Chesapeake Bay region. Auk 75:203-212."
[3] "Earnst, S.L. 1992. Behavior and ecology of Tundra Swans during summer, autumn, and winter. Ph.D. Thesis. Ohio State University."
$numRecords
[1] 54
$recordsPerSeason
Observation_Season n
1 5
2 multiple 11
3 winter 38
$recordsPerYearRegion
Location_Region 1956 1975 1992
1 Alaska NA NA 5
2 England NA 38 NA
3 United States 11 NA NA
$recordsPerPreyIDLevel
level n
1 Kingdom 0
2 Phylum 5
3 Class 0
4 Order 1
5 Suborder 0
6 Family 0
7 Genus 11
8 Species 37
$recordsPerType
Diet_Type n
1 Items 5
2 Occurrence 38
3 Wt_or_Vol 11
$analysesPerDietType
Diet_Type n
1 Items 1
2 Occurrence 1
3 Wt_or_Vol 1
$preySummary
Taxon Prey_Part Items Wt_or_Vol Occurrence
4 Magnoliopsida root; seed; vegetation 0.599 0.8597 0.0990
3 Cyanophyceae NA 0.232 NA NA
8 Unid. Tracheophyta vegetation 0.156 NA 0.0495
6 Unid. Arthropoda NA 0.013 NA NA
1 Bivalvia NA NA 0.1064 NA
2 Charophyceae gall NA 0.0338 NA
5 Polypodiopsida vegetation NA NA 0.0099
7 Unid. Chlorophyta vegetation NA NA 0.0198
> speciesSummary("Tundra swan", by = "Family")
$Studies
[1] "Owen, M. and C.J. Cadbury. 1975. The ecology and mortality of swans at the Ouse Washes, England. Wildfowl 26:31-42."
[2] "Stewart, R.E. and J.H. Manning. 1958. Distribution and ecology of Whistling Swans in the Chesapeake Bay region. Auk 75:203-212."
[3] "Earnst, S.L. 1992. Behavior and ecology of Tundra Swans during summer, autumn, and winter. Ph.D. Thesis. Ohio State University."
$numRecords
[1] 54
$recordsPerSeason
Observation_Season n
1 5
2 multiple 11
3 winter 38
$recordsPerYearRegion
Location_Region 1956 1975 1992
1 Alaska NA NA 5
2 England NA 38 NA
3 United States 11 NA NA
$recordsPerPreyIDLevel
level n
1 Kingdom 0
2 Phylum 5
3 Class 0
4 Order 1
5 Suborder 0
6 Family 0
7 Genus 11
8 Species 37
$recordsPerType
Diet_Type n
1 Items 5
2 Occurrence 38
3 Wt_or_Vol 11
$analysesPerDietType
Diet_Type n
1 Items 1
2 Occurrence 1
3 Wt_or_Vol 1
$preySummary
Taxon Prey_Part Items Wt_or_Vol Occurrence
5 Cyperaceae root; seed; vegetation 0.379 0.0819 0.0297
10 Nostocaceae NA 0.232 NA NA
14 Potamogetonaceae vegetation 0.220 0.0378 0.0099
24 Unid. Tracheophyta vegetation 0.156 NA 0.0495
21 Unid. Arthropoda NA 0.013 NA NA
1 Asteraceae root NA NA 0.0099
2 Boraginaceae vegetation NA NA 0.0099
3 Brassicaceae root NA NA 0.0396
4 Characeae gall NA 0.0338 NA
6 Equisetaceae vegetation NA NA 0.0099
7 Fabaceae seed; vegetation NA NA 0.0297
8 Hydrocharitaceae vegetation NA 0.3378 NA
9 Myidae NA NA 0.0276 NA
11 Plantaginaceae root; vegetation NA NA 0.0099
12 Poaceae seed; vegetation NA 0.0276 0.0990
13 Polygonaceae seed NA NA 0.0297
15 Ranunculaceae root; vegetation NA NA 0.0198
16 Rosaceae vegetation NA NA 0.0099
17 Ruppiaceae vegetation NA 0.3306 NA
18 Salicaceae vegetation NA NA 0.0099
19 Solanaceae root NA NA 0.0297
20 Tellinidae NA NA 0.0788 NA
22 Unid. Chlorophyta vegetation NA NA 0.0198
23 Unid. Poales root NA 0.0440 NA```
### dietSummary()
The `dietSummary()` function only returns the quantitative diet summary, but is more flexible with respect to specifying a season, region, set of years, or Diet\_Type of interest.
``` r
dietSummary("Bald Eagle", by = "Class", season = "winter", yearRange = c(1985, 2000), dietType = "Wt_or_Vol")
Taxon Prey_Part Frac_Diet
1 Aves NA 0.5710
2 Teleostei NA 0.3137
3 Mammalia NA 0.1157
dietSummary("Black-throated Blue Warbler", by = "Order", season = "summer", dietType = "Items")
Taxon Prey_Part Frac_Diet
1 Lepidoptera larva NA 0.5415
2 Coleoptera NA 0.2500
3 Diptera NA 0.0690
4 Lepidoptera NA 0.0690
5 Hemiptera NA 0.0260
6 Hymenoptera NA 0.0260
7 Araneae NA 0.0185
dietSummaryByPrey()
Finally, the dietSummaryByPrey() function provides a list of all bird species that consume a particular prey taxon in decreasing order of importance. In addition to providing the prey taxon name, you must also specify the taxonomic level of that name. Like the dietSummary() function you can filter results just to particular seasons, regions, years, or types of diet data.
There are two additional argument not present in dietSummary(). One is preyStage, which specifies the life stage of the prey item (if applicable) for which a summary should be conducted. By default ('any'), diet records will be included regardless of prey stage. Alternatively, one can specify that the summary should only be conducted for records including the terms 'larva', 'adult', or 'pupa' in the Diet Database's 'Prey_Stage' field. This is most relevant for Lepidoptera and a few other insect groups, where one might want to single out the importance of caterpillars or other larvae, for example.
This returns a summary at the level of individual studies, in which a single bird species might be listed multiple times because analyses were carried out in different, seasons, regions, years, etc.
caterpillars = dietSummaryByPrey("Lepidoptera", preyLevel = "Order", dietType = "Items", preyStage = "larva")
head(caterpillars, 10)
#> Common_Name Family Location_Region
#> 1 Oak Titmouse Paridae California
#> 2 Philadelphia Vireo Vireonidae New Hampshire
#> 3 Red-eyed Vireo Vireonidae New Hampshire
#> 4 Yellow-billed Cuckoo Cuculidae Puerto Rico
#> 5 Rose-breasted Grosbeak Cardinalidae New Hampshire
#> 6 Black-throated Green Warbler Parulidae New Hampshire
#> 7 Black-capped Chickadee Paridae West Virginia
#> 8 Black-throated Blue Warbler Parulidae New Hampshire
#> 9 Tennessee Warbler Parulidae Ontario
#> 10 Cape May Warbler Parulidae Ontario
#> Observation_Year_End Observation_Season Diet_Type Fraction_Diet Prey_Name
#> 1 1990 spring Items 0.8800000 Lepidoptera
#> 2 1979 summer Items 0.8730000 Lepidoptera
#> 3 1979 summer Items 0.8680000 Lepidoptera
#> 4 1912 summer Items 0.8333333 Lepidoptera
#> 5 1979 summer Items 0.8290000 Lepidoptera
#> 6 1979 summer Items 0.8280000 Lepidoptera
#> 7 1986 Summer Items 0.8152466 Lepidoptera
#> 8 1979 summer Items 0.8070000 Lepidoptera
#> 9 1994 summer Items 0.8020000 Lepidoptera
#> 10 1994 summer Items 0.7910000 Lepidoptera
#> Prey_Level Prey_Stage
#> 1 Order larva
#> 2 Order larva
#> 3 Order larva
#> 4 Order larva
#> 5 Order larva
#> 6 Order larva
#> 7 Order larva
#> 8 Order larva
#> 9 Order larva
#> 10 Order larva
By specifying speciesMean = TRUE, only a single value is returned for each bird species that is the average across all analyses meeting the season, region, and year criteria.
caterpillarsMean = dietSummaryByPrey("Lepidoptera", preyLevel = "Order", dietType = "Items",
preyStage = "larva", speciesMean = TRUE)
head(caterpillarsMean, 10)
#> Common_Name Family Diet_Type Fraction_Diet
#> 1 Philadelphia Vireo Vireonidae Items 0.6865000
#> 2 Oak Titmouse Paridae Items 0.6633333
#> 3 Black-throated Green Warbler Parulidae Items 0.5900000
#> 4 Blackburnian Warbler Parulidae Items 0.5732500
#> 5 Black-throated Blue Warbler Parulidae Items 0.5415000
#> 6 Cerulean Warbler Parulidae Items 0.5243750
#> 7 Rose-breasted Grosbeak Cardinalidae Items 0.4925000
#> 8 Cape May Warbler Parulidae Items 0.4835000
#> 9 Blue-headed Vireo Vireonidae Items 0.4784500
#> 10 Tennessee Warbler Parulidae Items 0.4718333
#> Prey_Name Prey_Level Prey_Stage
#> 1 Lepidoptera Order larva
#> 2 Lepidoptera Order larva
#> 3 Lepidoptera Order larva
#> 4 Lepidoptera Order larva
#> 5 Lepidoptera Order larva
#> 6 Lepidoptera Order larva
#> 7 Lepidoptera Order larva
#> 8 Lepidoptera Order larva
#> 9 Lepidoptera Order larva
#> 10 Lepidoptera Order larva
Final thoughts
-
If you have any suggestions on the package please feel free to post an issue.
-
Citation: Hurlbert, AH, AM Olsen, MM Sawyer, and PM Winner. 2021. The Avian Diet Database as a quantitative source of information on avian diets. Scientific Data 8:260. https://doi.org/10.1038/s41597-021-01049-9
-
If you are aware of a quantitative study on avian diets that is NOT in the database (especially for North American species), please post an issue in the Avian Diet Database development repo with "study with diet data -- [Author Year]" as the subject line.
ahhurlbert/aviandietdb documentation built on Oct. 12, 2021, 5:20 p.m.
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aviandietdb
aviandietdb provides access to the Avian Diet Database, which contains quantitative diet data for bird species as well as contextual information about where and when those data were collected.
The archived database currently includes 73,075 diet records for 759 bird species. This is a growing database, and while it is currently North American biased, we hope to continue adding avian diet data from around the world.
You can find the development version of the database (which may include more recent records than what is available in the R package but which may still require data cleaning) here.
This R package provides a few simple functions for summarizing and querying the database.
Installation
You can install aviandietdb from GitHub with:
# install.packages("devtools")
devtools::install_github("ahhurlbert/aviandietdb")
Database
Load the library and then the R data file that contains the raw data.
library(aviandietdb)
data(dietdb)
Typing ?dietdb will provide a description of the 42 data fields in this database.
A summary of the total number of records by species, and the total number of species with data by family is provided using dbSummary().
dbSummary()
#> $numRecords
#> [1] 73075
#>
#> $numSpecies
#> [1] 759
#>
#> $numStudies
#> [1] 993
#>
#> $recordsPerSpecies
#> # A tibble: 600 x 3
#> Common_Name Family n
#> <chr> <chr> <int>
#> 1 Abert's Towhee Passerellidae 17
#> 2 Acadian Flycatcher Tyrannidae 150
#> 3 Acorn Woodpecker Picidae 70
#> 4 Adelaide's Warbler Parulidae 34
#> 5 African Pygmy-Goose Anatidae 10
#> 6 Alder/Willow Flycatcher (Traill's Flycatcher) Tyrannidae 87
#> 7 American Avocet Recurvirostridae 8
#> 8 American Black Duck Anatidae 51
#> 9 American Coot Rallidae 198
#> 10 American Crow Corvidae 225
#> # ... with 590 more rows
#>
#> $speciesPerFamily
#> # A tibble: 99 x 5
#> Order Family SpeciesWithData TotalSpeciesABA PercentComplete
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 Accipitriformes Accipitridae 25 35 71
#> 2 Accipitriformes Pandionidae 1 1 100
#> 3 Anseriformes Anatidae 102 116 88
#> 4 Bucerotiformes Upupidae 0 1 0
#> 5 Caprimulgiformes Apodidae 2 10 20
#> 6 Caprimulgiformes Caprimulgidae 5 10 50
#> 7 Caprimulgiformes Trochilidae 16 34 47
#> 8 Cathartiformes Cathartidae 3 4 75
#> 9 Charadriiformes Alcidae 2 23 9
#> 10 Charadriiformes Charadriidae 1 17 6
#> # ... with 89 more rows
Diet_Type
When examining these diet data it is important to understand the different possible ways that investigators may have quantified the importance of different diet items, because these different methods are not necessarily comparable with each other. This means any summaries will be specific to a particular 'Diet_Type'. In this database, the possible values are:
- Items - the fraction of the diet based on the proportion of total diet items examined (e.g. 9 out of 12 prey items examined were ants);
- Wt_or_Vol - the fraction of the diet based on the proportional weight or volume of the prey taxa examined (e.g. ants made up 10% of the diet by mass);
- Occurrence - the proportion of bird specimens (e.g. stomachs, nests, fecal samples) that included at least one of the specified prey taxa (e.g. ants occurred in 90% of stomachs examined); NOTE: this is the one measure that need not sum to 100% across diet items within a given analysis;
- Unspecified - in the event that it is unclear from the Methods section of the study which measure was being used, it is listed as "Unspecified"
Summary functions
For now, we provide just three simple ways to summarize data from the Diet Database.
speciesSummary()
The speciesSummary() function provides a summary of what kinds of data are available for the specified bird species, as well as a quantitative summary at the taxonomic level specified. In the example below, you can see (1) the list of all studies providing quantitative diet data, (2) the total number of diet records, (3) the distribution of those records seasonally, (4) the distribution of those records across years and states/provinces, (5) the distribution of records by the taxonomic level to which prey were identified, (6) the distribution of records by Diet_Type, (7) the total number of diet analyses conducted for each Diet_Type, and (8) a quantitative summary of the diet at the specified taxonomic level averaged across all available studies of a given Diet_Type. If the original data source indicated that specific parts of the prey taxon was consumed (e.g. fruit, seed, vegetation, etc.) then they are listed in the Prey_Part field.
> speciesSummary("Tundra swan", by = "Class")
$Studies
[1] "Owen, M. and C.J. Cadbury. 1975. The ecology and mortality of swans at the Ouse Washes, England. Wildfowl 26:31-42."
[2] "Stewart, R.E. and J.H. Manning. 1958. Distribution and ecology of Whistling Swans in the Chesapeake Bay region. Auk 75:203-212."
[3] "Earnst, S.L. 1992. Behavior and ecology of Tundra Swans during summer, autumn, and winter. Ph.D. Thesis. Ohio State University."
$numRecords
[1] 54
$recordsPerSeason
Observation_Season n
1 5
2 multiple 11
3 winter 38
$recordsPerYearRegion
Location_Region 1956 1975 1992
1 Alaska NA NA 5
2 England NA 38 NA
3 United States 11 NA NA
$recordsPerPreyIDLevel
level n
1 Kingdom 0
2 Phylum 5
3 Class 0
4 Order 1
5 Suborder 0
6 Family 0
7 Genus 11
8 Species 37
$recordsPerType
Diet_Type n
1 Items 5
2 Occurrence 38
3 Wt_or_Vol 11
$analysesPerDietType
Diet_Type n
1 Items 1
2 Occurrence 1
3 Wt_or_Vol 1
$preySummary
Taxon Prey_Part Items Wt_or_Vol Occurrence
4 Magnoliopsida root; seed; vegetation 0.599 0.8597 0.0990
3 Cyanophyceae NA 0.232 NA NA
8 Unid. Tracheophyta vegetation 0.156 NA 0.0495
6 Unid. Arthropoda NA 0.013 NA NA
1 Bivalvia NA NA 0.1064 NA
2 Charophyceae gall NA 0.0338 NA
5 Polypodiopsida vegetation NA NA 0.0099
7 Unid. Chlorophyta vegetation NA NA 0.0198
> speciesSummary("Tundra swan", by = "Family")
$Studies
[1] "Owen, M. and C.J. Cadbury. 1975. The ecology and mortality of swans at the Ouse Washes, England. Wildfowl 26:31-42."
[2] "Stewart, R.E. and J.H. Manning. 1958. Distribution and ecology of Whistling Swans in the Chesapeake Bay region. Auk 75:203-212."
[3] "Earnst, S.L. 1992. Behavior and ecology of Tundra Swans during summer, autumn, and winter. Ph.D. Thesis. Ohio State University."
$numRecords
[1] 54
$recordsPerSeason
Observation_Season n
1 5
2 multiple 11
3 winter 38
$recordsPerYearRegion
Location_Region 1956 1975 1992
1 Alaska NA NA 5
2 England NA 38 NA
3 United States 11 NA NA
$recordsPerPreyIDLevel
level n
1 Kingdom 0
2 Phylum 5
3 Class 0
4 Order 1
5 Suborder 0
6 Family 0
7 Genus 11
8 Species 37
$recordsPerType
Diet_Type n
1 Items 5
2 Occurrence 38
3 Wt_or_Vol 11
$analysesPerDietType
Diet_Type n
1 Items 1
2 Occurrence 1
3 Wt_or_Vol 1
$preySummary
Taxon Prey_Part Items Wt_or_Vol Occurrence
5 Cyperaceae root; seed; vegetation 0.379 0.0819 0.0297
10 Nostocaceae NA 0.232 NA NA
14 Potamogetonaceae vegetation 0.220 0.0378 0.0099
24 Unid. Tracheophyta vegetation 0.156 NA 0.0495
21 Unid. Arthropoda NA 0.013 NA NA
1 Asteraceae root NA NA 0.0099
2 Boraginaceae vegetation NA NA 0.0099
3 Brassicaceae root NA NA 0.0396
4 Characeae gall NA 0.0338 NA
6 Equisetaceae vegetation NA NA 0.0099
7 Fabaceae seed; vegetation NA NA 0.0297
8 Hydrocharitaceae vegetation NA 0.3378 NA
9 Myidae NA NA 0.0276 NA
11 Plantaginaceae root; vegetation NA NA 0.0099
12 Poaceae seed; vegetation NA 0.0276 0.0990
13 Polygonaceae seed NA NA 0.0297
15 Ranunculaceae root; vegetation NA NA 0.0198
16 Rosaceae vegetation NA NA 0.0099
17 Ruppiaceae vegetation NA 0.3306 NA
18 Salicaceae vegetation NA NA 0.0099
19 Solanaceae root NA NA 0.0297
20 Tellinidae NA NA 0.0788 NA
22 Unid. Chlorophyta vegetation NA NA 0.0198
23 Unid. Poales root NA 0.0440 NA```
### dietSummary()
The `dietSummary()` function only returns the quantitative diet summary, but is more flexible with respect to specifying a season, region, set of years, or Diet\_Type of interest.
``` r
dietSummary("Bald Eagle", by = "Class", season = "winter", yearRange = c(1985, 2000), dietType = "Wt_or_Vol")
Taxon Prey_Part Frac_Diet
1 Aves NA 0.5710
2 Teleostei NA 0.3137
3 Mammalia NA 0.1157
dietSummary("Black-throated Blue Warbler", by = "Order", season = "summer", dietType = "Items")
Taxon Prey_Part Frac_Diet
1 Lepidoptera larva NA 0.5415
2 Coleoptera NA 0.2500
3 Diptera NA 0.0690
4 Lepidoptera NA 0.0690
5 Hemiptera NA 0.0260
6 Hymenoptera NA 0.0260
7 Araneae NA 0.0185
dietSummaryByPrey()
Finally, the dietSummaryByPrey() function provides a list of all bird species that consume a particular prey taxon in decreasing order of importance. In addition to providing the prey taxon name, you must also specify the taxonomic level of that name. Like the dietSummary() function you can filter results just to particular seasons, regions, years, or types of diet data.
There are two additional argument not present in dietSummary(). One is preyStage, which specifies the life stage of the prey item (if applicable) for which a summary should be conducted. By default ('any'), diet records will be included regardless of prey stage. Alternatively, one can specify that the summary should only be conducted for records including the terms 'larva', 'adult', or 'pupa' in the Diet Database's 'Prey_Stage' field. This is most relevant for Lepidoptera and a few other insect groups, where one might want to single out the importance of caterpillars or other larvae, for example.
This returns a summary at the level of individual studies, in which a single bird species might be listed multiple times because analyses were carried out in different, seasons, regions, years, etc.
caterpillars = dietSummaryByPrey("Lepidoptera", preyLevel = "Order", dietType = "Items", preyStage = "larva")
head(caterpillars, 10)
#> Common_Name Family Location_Region
#> 1 Oak Titmouse Paridae California
#> 2 Philadelphia Vireo Vireonidae New Hampshire
#> 3 Red-eyed Vireo Vireonidae New Hampshire
#> 4 Yellow-billed Cuckoo Cuculidae Puerto Rico
#> 5 Rose-breasted Grosbeak Cardinalidae New Hampshire
#> 6 Black-throated Green Warbler Parulidae New Hampshire
#> 7 Black-capped Chickadee Paridae West Virginia
#> 8 Black-throated Blue Warbler Parulidae New Hampshire
#> 9 Tennessee Warbler Parulidae Ontario
#> 10 Cape May Warbler Parulidae Ontario
#> Observation_Year_End Observation_Season Diet_Type Fraction_Diet Prey_Name
#> 1 1990 spring Items 0.8800000 Lepidoptera
#> 2 1979 summer Items 0.8730000 Lepidoptera
#> 3 1979 summer Items 0.8680000 Lepidoptera
#> 4 1912 summer Items 0.8333333 Lepidoptera
#> 5 1979 summer Items 0.8290000 Lepidoptera
#> 6 1979 summer Items 0.8280000 Lepidoptera
#> 7 1986 Summer Items 0.8152466 Lepidoptera
#> 8 1979 summer Items 0.8070000 Lepidoptera
#> 9 1994 summer Items 0.8020000 Lepidoptera
#> 10 1994 summer Items 0.7910000 Lepidoptera
#> Prey_Level Prey_Stage
#> 1 Order larva
#> 2 Order larva
#> 3 Order larva
#> 4 Order larva
#> 5 Order larva
#> 6 Order larva
#> 7 Order larva
#> 8 Order larva
#> 9 Order larva
#> 10 Order larva
By specifying speciesMean = TRUE, only a single value is returned for each bird species that is the average across all analyses meeting the season, region, and year criteria.
caterpillarsMean = dietSummaryByPrey("Lepidoptera", preyLevel = "Order", dietType = "Items",
preyStage = "larva", speciesMean = TRUE)
head(caterpillarsMean, 10)
#> Common_Name Family Diet_Type Fraction_Diet
#> 1 Philadelphia Vireo Vireonidae Items 0.6865000
#> 2 Oak Titmouse Paridae Items 0.6633333
#> 3 Black-throated Green Warbler Parulidae Items 0.5900000
#> 4 Blackburnian Warbler Parulidae Items 0.5732500
#> 5 Black-throated Blue Warbler Parulidae Items 0.5415000
#> 6 Cerulean Warbler Parulidae Items 0.5243750
#> 7 Rose-breasted Grosbeak Cardinalidae Items 0.4925000
#> 8 Cape May Warbler Parulidae Items 0.4835000
#> 9 Blue-headed Vireo Vireonidae Items 0.4784500
#> 10 Tennessee Warbler Parulidae Items 0.4718333
#> Prey_Name Prey_Level Prey_Stage
#> 1 Lepidoptera Order larva
#> 2 Lepidoptera Order larva
#> 3 Lepidoptera Order larva
#> 4 Lepidoptera Order larva
#> 5 Lepidoptera Order larva
#> 6 Lepidoptera Order larva
#> 7 Lepidoptera Order larva
#> 8 Lepidoptera Order larva
#> 9 Lepidoptera Order larva
#> 10 Lepidoptera Order larva
Final thoughts
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If you have any suggestions on the package please feel free to post an issue.
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Citation: Hurlbert, AH, AM Olsen, MM Sawyer, and PM Winner. 2021. The Avian Diet Database as a quantitative source of information on avian diets. Scientific Data 8:260. https://doi.org/10.1038/s41597-021-01049-9
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If you are aware of a quantitative study on avian diets that is NOT in the database (especially for North American species), please post an issue in the Avian Diet Database development repo with "study with diet data -- [Author Year]" as the subject line.
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