diet: SquamataBase
In blueraleigh/squamatabase: squamatabase

diet	R Documentation

SquamataBase

Description

A database of prey items in diet samples from the world's snakes

Usage

diet

Format

An object of class data.frame with 10938 rows and 38 columns.

Compilation methods

I compiled SquamataBase from numerous articles published in scientific journals. I located material both through the use of keyword queries in academic search engines and by systematic review of table of contents for well-known herpetological journals (e.g. Herpetological Review, Herpetology Notes). I also located additional relevant articles by consulting the references in reviewed articles. My goal was simply to track down as many relevant sources as possible. The current compilation includes data from approximately 1700 different sources but remains incomplete in many ways (e.g., geographically and taxonomically).

The majority of observations in the database result from papers describing (1) dissections of fluid preserved museum specimens and (2) direct encounters with snakes in the field that were actively consuming a prey or had recently consumed a prey item that could be regurgitated by forced palpation. Glaudas et al. (2017) have noted that these sources of information can provide different pictures of the prey spectrum for Bitis arietans (Puff Adder).

Database fields

Each record in the database describes a snake specimen eating or attempting to eat a prey specimen. Note that due to the nature of the published data a "specimen" does not necessarily correspond to a single individual. In all cases, however, a specimen refers to a set of individuals that belong to the same taxon. The following fields are associated with each record:

predator_verbatim: The scientific name of the predator as reported by the original authors.
predator: The scientific name the predator according to the 2016 Catalogue of Life taxonomy.
predator_rank: The Linnean rank of the predator. Typically this will be "species" or "infraspecies".
predator_taxon: A semicolon separated list of the higher taxonomic names that apply to the predator.
predator_count: The number of individual predator organisms involved in the interaction.
predator_voucher: A unique identifier for the specimen that is either (1) a bona fide museum voucher number or (2) a randomly generated alphanumeric code. The rationale for this field is that same predator specimen may have eaten multiple prey specimens that carry unique identifying information (e.g. taxonomic identities, distinct ages, etc.), in which case each prey specimen requires its own row, thus necessitating duplication of the predator specimen across rows. Having a unique identifier for the predator specimen allows one to identify the same predator specimen appearing in multiple rows, although this rarely happens due to the tendency of snakes to only have a single prey item in their gut. A caveat needs to be mentioned. In many cases, the results of museum studies are reported in summarized tabular form. For example, a museum study of snake X may report that 12 specimens had eaten 14 individuals of prey Y and that 8 specimens had eaten 8 individuals of prey Z. These data will be represented in SquamataBase as two rows, and each row will have a unique randomly generated predator_voucher. This is because there is no way, without further information, to know whether any of the individuals eating prey Y also ate prey Z.
predator_sex: The sex of the specimen. Typically only used when the predator_count field is 1.
predator_age: The age of the specimen.Typically only used when the predator_count field is 1.
predator_svl: The snout-vent-length (in mm) of the specimen. Typically only used when the predator_count field is 1.
predator_tl: The total length (in mm) of the specimen. Typically only used when the predator_count field is 1.
predator_mass: The mass (in grams) of the specimen. Typically only used when the predator_count field is 1.
NOTE: All of the above fields with the exception of the svl field are also recorded for the prey specimen, and hence take the prefix "prey". Additionally, the following field is unique to the prey specimen:
prey_ingested: The orientation in which the prey specimen was swallowed. Typically only used when the prey_count field is 1.
locality_adm0_name: The country where the predation event occurred.
locality_adm1_name: The state where the predation event occurred.
locality_adm2_name: The county where the predation event occurred.
locality_longitude: Decimal longitude where the predation event occurred.
locality_latitude: Decimal latitude where the predation event occurred.
event_basis: Evidentiary basis for the reported predation event. Typically "direct_observation" or "dissected_gut_contents".
event_setting: A note indicating whether the predation event was observed in a natural or a captive setting. Almost all records in the database are recorded from natural settings. Observations resulting from dissections of museum specimens are assumed to have occurred in a natural setting.
event_date: YYYY-MM-DD formatted date when the predation event was observed. If the observation resulted from an examination of gut contents this field is the collection date of the specimen.
event_start: HH:MM formatted time when the predation event was first noted, measured on a 24 hour clock to avoid AM and PM designations.
event_end: HH:MM formatted time when the predation event ended, measured on a 24 hour clock to avoid AM and PM designations.
event_outcome: If the predation event was successful this field takes the value "prey_eaten". This is always the case if the observation is based on dissections of museum specimens. However, for observations based on encounters with snakes in the field other outcomes are possible and the values in this field are self-explanatory (e.g. "predation_interrupted_by_observer").
event_habitat: A simple habitat descriptor indicating whether the predation occurred in a terrestrial, fossorial, arboreal, or aquatic setting.
event_habitat_verbatim: Habitat description in the words of the original authors.
event_remark: Miscellaneous narrative information regarded as potentially relevant.
reference: Bibliographic citation to the original source of the record.