The goal of seabirddietDB is to provide access and tools to interact with a database of seabird diets collected around the British Isles.
You can install the development version from GitHub with:
# install.packages("remotes")
remotes::install_github("annakrystalli/seabirddietDB")
For more details on the dataset, check out the full documentation
To access the data simply load the package. The data is then available
library(seabirddietDB)
seabirddiet
#> # A tibble: 2,857 x 33
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 1 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 2 2 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 3 3 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 4 4 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 5 5 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 6 6 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 7 7 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 8 8 1983 1983 1983 FALSE East An… 52.5 1
#> 9 9 1983 1983 1983 FALSE East An… 52.5 1
#> 10 10 1983 1983 1983 FALSE East An… 52.5 1
#> # … with 2,847 more rows, and 25 more variables: pred_common_name <chr>,
#> # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>,
#> # pred_valid_name <chr>, pred_valid_aphia_id <int>,
#> # pred_breeding_status <chr>, pred_age_group <chr>,
#> # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>,
#> # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>,
#> # prey_size <chr>, prey_age_group <chr>, freq_occ <dbl>, freq_num <dbl>,
#> # freq_biomass <dbl>, sample_size <dbl>, sample_type <chr>, ref_n <dbl>,
#> # ref_ids <chr>, source <chr>, notes <chr>
A version with more formal data types/structures in the columns (ie
geographic information stored as sf
, categorical data as factors etc)
is also available. Note that you will need package sf
installed to
load this version of the data.
class(seabirddiet_)
A number of metadata datasets are included with the package:
attributes
, references
and classification
. Load them as you would
one of the datasets, e.g. :
references
#> # A tibble: 97 x 2
#> ref_id ref_valid
#> <chr> <chr>
#> 1 REF001 Anderson et al 2014 Ibis 156, 23-34
#> 2 REF002 Bailey et al 1991 ICES Mar. Sci. Symp., 193, 209-216
#> 3 REF003 Baker et 1999 JNCC Report 289, 1-51
#> 4 REF004 Blake BF 1984 J. Experimental. Mar.Biol. Ecol. 76, 89-103
#> 5 REF005 Blake et al 1955 Estuarine, Coastal & Shelf Science 20, 559-568
#> 6 REF006 Blake et al 1980 Unpubl NCC Report
#> 7 REF007 Blake et al 1985 Estuarine, Coastal & Shelf Science 20, 559-568
#> 8 REF008 Bull et al 2001 JNCC Report, No. 303
#> 9 REF009 Bull et al 2001 JNCC Report, No. 315
#> 10 REF010 Bull et al 2004 Ardea 92, 43-52
#> # … with 87 more rows
List predators
sbd_predators()
#> [1] "Alca torda" "Fratercula arctica"
#> [3] "Fulmarus glacialis" "Morus bassanus"
#> [5] "Phalacrocorax aristotelis" "Puffinus puffinus"
#> [7] "Rissa tridactyla" "Uria aalge"
List prey
sbd_prey(verbose = TRUE)
#> # A tibble: 129 x 5
#> prey_taxon prey_rank prey_aphia_id prey_valid_name prey_valid_aphi…
#> <chr> <chr> <int> <chr> <int>
#> 1 Acanthephyra genus 107018 Acanthephyra 107018
#> 2 Acanthephyra… species 107581 Acanthephyra pel… 107581
#> 3 Actinopteryg… class 10194 Actinopterygii 10194
#> 4 Agonidae family 125588 Agonidae 125588
#> 5 Agonus catap… species 127190 Agonus cataphrac… 127190
#> 6 Alloteuthis … species 153131 Alloteuthis subu… 153131
#> 7 Ammodytes la… species 146485 Hyperoplus lance… 126756
#> 8 Ammodytes ma… species 126751 Ammodytes marinus 126751
#> 9 Ammodytes to… species 126752 Ammodytes tobian… 126752
#> 10 Ammodytidae family 125516 Ammodytidae 125516
#> # … with 119 more rows
sbd_filter(pred_species = "Fratercula arctica")
#> # A tibble: 615 x 33
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 1 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 2 2 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 3 3 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 4 4 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 5 5 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 6 6 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 7 7 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 8 8 1983 1983 1983 FALSE East An… 52.5 1
#> 9 9 1983 1983 1983 FALSE East An… 52.5 1
#> 10 10 1983 1983 1983 FALSE East An… 52.5 1
#> # … with 605 more rows, and 25 more variables: pred_common_name <chr>,
#> # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>,
#> # pred_valid_name <chr>, pred_valid_aphia_id <int>,
#> # pred_breeding_status <chr>, pred_age_group <chr>,
#> # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>,
#> # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>,
#> # prey_size <chr>, prey_age_group <chr>, freq_occ <dbl>, freq_num <dbl>,
#> # freq_biomass <dbl>, sample_size <dbl>, sample_type <chr>, ref_n <dbl>,
#> # ref_ids <chr>, source <chr>, notes <chr>
sbd_filter(pred_species = "Fratercula arctica", metrics = "freq_biomass")
#> # A tibble: 219 x 31
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 291 1973 1973 1973 FALSE Isle of… 56.2 -2.56
#> 2 292 1973 1973 1973 FALSE Isle of… 56.2 -2.56
#> 3 293 1973 1973 1973 FALSE Isle of… 56.2 -2.56
#> 4 298 1973 1973 1973 FALSE Isle of… 56.2 -2.56
#> 5 299 1973 1973 1973 FALSE Isle of… 56.2 -2.56
#> 6 300 1974 1974 1974 FALSE Isle of… 56.2 -2.56
#> 7 301 1974 1974 1974 FALSE Isle of… 56.2 -2.56
#> 8 308 1974 1974 1974 FALSE Isle of… 56.2 -2.56
#> 9 309 1974 1974 1974 FALSE Isle of… 56.2 -2.56
#> 10 310 1975 1975 1975 FALSE Isle of… 56.2 -2.56
#> # … with 209 more rows, and 23 more variables: pred_common_name <chr>,
#> # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>,
#> # pred_valid_name <chr>, pred_valid_aphia_id <int>,
#> # pred_breeding_status <chr>, pred_age_group <chr>,
#> # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>,
#> # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>,
#> # prey_size <chr>, prey_age_group <chr>, freq_biomass <dbl>,
#> # sample_size <dbl>, sample_type <chr>, ref_n <dbl>, ref_ids <chr>,
#> # source <chr>, notes <chr>
sbd_filter(prey_taxon = c("Cottidae", "Actinopterygii"))
#> # A tibble: 124 x 33
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 360 1982 1982 1982 FALSE Isle of… 56.2 -2.56
#> 2 366 1983 1983 1983 FALSE Isle of… 56.2 -2.56
#> 3 374 1984 1984 1984 FALSE Isle of… 56.2 -2.56
#> 4 899 1990 1990 1990 FALSE Isle of… 56.2 -2.56
#> 5 911 1992 1992 1992 FALSE Isle of… 56.2 -2.56
#> 6 1055 2006 2006 2006 FALSE Isle of… 56.2 -2.56
#> 7 1197 2009 2006 2011 TRUE Anglesey 53.3 -4.43
#> 8 1201 2009 2006 2011 TRUE Bempton 54.1 -0.17
#> 9 1214 2009 2006 2011 TRUE Bullers… 57.4 -1.82
#> 10 1218 2009 2006 2011 TRUE Burravoe 60.6 -1.05
#> # … with 114 more rows, and 25 more variables: pred_common_name <chr>,
#> # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>,
#> # pred_valid_name <chr>, pred_valid_aphia_id <int>,
#> # pred_breeding_status <chr>, pred_age_group <chr>,
#> # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>,
#> # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>,
#> # prey_size <chr>, prey_age_group <chr>, freq_occ <dbl>, freq_num <dbl>,
#> # freq_biomass <dbl>, sample_size <dbl>, sample_type <chr>, ref_n <dbl>,
#> # ref_ids <chr>, source <chr>, notes <chr>
sbd_filter(year = 1973:1976)
#> # A tibble: 207 x 33
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 1 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 2 2 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 3 3 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 4 4 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 5 5 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 6 6 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 7 7 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 8 11 1974 1974 1974 FALSE Fair Is… 59.6 -1.63
#> 9 12 1974 1974 1974 FALSE Fair Is… 59.6 -1.63
#> 10 13 1974 1974 1974 FALSE Fair Is… 59.6 -1.63
#> # … with 197 more rows, and 25 more variables: pred_common_name <chr>,
#> # pred_species <chr>, pred_rank <chr>, pred_aphia_id <int>,
#> # pred_valid_name <chr>, pred_valid_aphia_id <int>,
#> # pred_breeding_status <chr>, pred_age_group <chr>,
#> # prey_orig_descr <chr>, prey_taxon <chr>, prey_rank <chr>,
#> # prey_aphia_id <int>, prey_valid_name <chr>, prey_valid_aphia_id <int>,
#> # prey_size <chr>, prey_age_group <chr>, freq_occ <dbl>, freq_num <dbl>,
#> # freq_biomass <dbl>, sample_size <dbl>, sample_type <chr>, ref_n <dbl>,
#> # ref_ids <chr>, source <chr>, notes <chr>
sbd_filter(year = 1973:1976, pred_species = "Uria aalge", prey_taxon = "Gadidae")
#> # A tibble: 3 x 33
#> id year startyear endyear multiyear location latitude longitude
#> <int> <dbl> <dbl> <dbl> <lgl> <chr> <dbl> <dbl>
#> 1 1333 1973 1973 1973 FALSE Co. Ker… 52.2 -9.75
#> 2 1699 1973 1973 1973 FALSE Skomer 51.6 -5.29
#> 3 1704 1975 1975 1975 FALSE Skomer 51.6 -5.29
#> # … with 25 more variables: pred_common_name <chr>, pred_species <chr>,
#> # pred_rank <chr>, pred_aphia_id <int>, pred_valid_name <chr>,
#> # pred_valid_aphia_id <int>, pred_breeding_status <chr>,
#> # pred_age_group <chr>, prey_orig_descr <chr>, prey_taxon <chr>,
#> # prey_rank <chr>, prey_aphia_id <int>, prey_valid_name <chr>,
#> # prey_valid_aphia_id <int>, prey_size <chr>, prey_age_group <chr>,
#> # freq_occ <dbl>, freq_num <dbl>, freq_biomass <dbl>, sample_size <dbl>,
#> # sample_type <chr>, ref_n <dbl>, ref_ids <chr>, source <chr>,
#> # notes <chr>
There are additional helpers for interactive plotting of data
sbd_plot_predators(year = 1973)
To cite use
citation("seabirddietDB")
#>
#> To cite package 'seabirddietDB' in publications use:
#>
#> Anna Krystalli, Agnes Olin, James Grecian and Ruedi Nager
#> (2019). seabirddietDB: Seabird Diet Database. R package version
#> 0.0.1. https://github.com/annakrystalli/seabirddietDB
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {seabirddietDB: Seabird Diet Database},
#> author = {Anna Krystalli and Agnes Olin and James Grecian and Ruedi Nager},
#> year = {2019},
#> note = {R package version 0.0.1},
#> url = {https://github.com/annakrystalli/seabirddietDB},
#> }
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