setup_list: Create a list object to request download of species register

In diogosbr/splink: Interface to the speciesLink API

Create a list object to request download of species register

Description

This function prepare a list to request download of species register with the get_data function.

Usage

setup_list(
  ScientificName = NULL,
  Barcode = NULL,
  BasisOfRecord = NULL,
  CollectionCode = NULL,
  CatalogNumber = NULL,
  Collector = NULL,
  CollectorNumber = NULL,
  YearCollected = NULL,
  IdentifiedBy = NULL,
  YearIdentified = NULL,
  Kingdom = NULL,
  Phylum = NULL,
  Class = NULL,
  Order = NULL,
  Family = NULL,
  Genus = NULL,
  TypeStatus = NULL,
  Country = NULL,
  StateProvince = NULL,
  County = NULL,
  Locality = NULL,
  Notes = NULL,
  MaxRecords = NULL,
  Model = NULL,
  Phonetic = NULL,
  RedList = NULL,
  Scope = NULL,
  Coordinates = NULL,
  Images = NULL,
  Synonyms = NULL,
  Typus = NULL
)

Arguments

ScientificName	A character vector with scientific name, without authors. Accepts a vector of names. If you want include synonym taxa use Synonyms argument. See details to use 'embranco' or "naobranco" options.
Barcode	Barcode of specimen in a collection. Ex: NY00000001 or FPS00257.
BasisOfRecord	Values accepted: 'PreservedSpecimen' , 'LivingSpecimen', 'FossilSpecimen', 'HumanObservation', 'MachineObservation' or 'MaterialSample'.
CollectionCode	Collection acronym to search. Ex: "FIOCRUZ-CEIOC", "UEC", "HUEFS".
CatalogNumber	Register number of specimen in the collection.
Collector	Collector name. Ex: "Kock", "Almeida F".
CollectorNumber	Collector number.
YearCollected	Year of specimen was collected with four-digits. Accepts a vector.
IdentifiedBy	Who identified the species of specimen. Ex: "Abreu MC".
YearIdentified	Year of specimen was identified with four-digits.
Kingdom	Kingdom classification name.
Phylum	Phylum classification name.
Class	Class classification name.
Order	Order classification name.
Family	Family classification name.
Genus	Genus classification name.
TypeStatus	.
Country	Country of specimen register.
StateProvince	State of specimen register.
County	City of specimen register.
Locality	Locality of specimen register. This field is very dificult to return with precision because it is a free form field.
Notes	String.
MaxRecords	numeric. The maximum number of general records to be returned. Default is to return all records. See details for more information.
Model	String. "DwC" is default and will return all DwC records. "coords" will return coordinates only.
Phonetic	Logical. If TRUE, allows the system to ignore some spelling differences in scientific names like 'Y' or 'I', double letters, etc. Affects only taxonomic fields Phylum, Class, Order, Family e ScientificName. FALSE is default.
RedList	Searches for records with scientific names that appear in red list of MMA if 'yes' or it that not appear in red list of MMA if 'no'. To return any records the values is NULL (default).
Scope	Groups of organisms to search. The accepted values are "plants", "animals", "microrganisms" and "fossils". NULL to search in all groups (default).
Coordinates	Choose if will download the registers with coordinates. Default is all registers (with coordinates or not). See details for available options. ('Yes' , 'No' , 'Original' , 'Automatic' , 'Blocked')
Images	If NULL (default) will search all record. If "yes" search the records that contain images of the specimen and 'no' will return only records without images. Images will not be downloaded. For more options see Details.
Synonyms	Search also for synonyms defined in the following dictionaries: "sp2000", "flora2020", "MycoBank", "AlgaeBase", "DSMZ", "Moure" and/or NULL (default) if you don't want to search for synonyms.
Typus	If 'yes' searches for type material only. If 'no', searches non type material only. Default is NULL and does no check type material.

Details

For more information about fields see https://api.splink.org.br/ , http://www.splink.org.br/ , https://www.youtube.com/watch?v=I-4ftIWrKUA&feature=youtu.be or http://www.splink.org.br/showTips.

The search system is case insensitive, meaning that searching for Tabeuia aurea is the same as searching for tabebuia aurea or TABEBUIA AUREA.

Accents are also not considered, meaning searching for São Paulo is the same as searching for Sao Paulo.

Avoid using words such as de, do, em, the, etc. For example when searching for species that occur in Serra da Canastra, search for Serra Canastra or just Canastra within the locality field.

In general, all words included in the form are considered when searching. Searching for Souza Silva in the collector’s field will retrieve all records that have the words Souza AND Silva simultaneously in that field.

Besides the connector |, users may search for a list of species – one in each line – with a maximum limit of 50 names.

Users can also search for blank fields, by typing the word null in the field. For example, to search for unidentified material of the family Asteraceae, users must type Asteraceae in the family field and null in the scientific name field. Also for Asteracea, if you want to see what genera of the Asteraceae family have unidentified material, you may type notnull null in the scientific name field. The words null and notnull can be used in other fields.

The words 'null' and 'notnull' can also be used in the scientific name field. It is important to remember that the scientific name can be a genus (a single word), a binomial (genus + species) or a trinomial (genus + species + subspecies). The words 'null' and 'notnull' can replace any of these elements. For example: to search for records that have identification only up to the gender level, type 'notnull null' in the scientific name field.

Nos campos buscadores são aceitos valores 'embranco' ou 'naobranco'. Por exemplo: é possível buscar apenas os registros de um gênero que não tenha sido identificado ainda, para isso deve-se informar no campo ScientificName "Manilkara embranco" (para o gênero Manilkara). Em caso de querer apenas os registros de um gênero que tenha identificação deve-se informar "Manilkara naobranco". No caso de querer todos os registros de um gênero, basta colocar "Manilkara".

Coordinates: Yes | No | Original | Automatic | Blocked no check.

The complete list of searchable and modifiers fields are available with fields_data() (not implemented yet) function.

Attention, because the MaxRecords refers to the total number of records, in case of searching for more than one species it may be that records of only one species are returned. This depends on the number of records per species and the maximum number of records requested.

To the Images argument, the options are "yes" for records with images, "no" for records without images, "live" for records with images of living material, "pollen" for records with images of pollen, "wood" for images of wood (Xylotheque) and NULL to search all records.

Value

A list with parameters to use in get_data() function to download records.

Examples

setup_list(ScientificName = "Manilkara maxima")

## Not run: 
setup_list(ScientificName = c("Rauvolfia sellowii", "Cantinoa althaeifolia"),
           StateProvince = c("São Paulo","Rio de Janeiro","Pernambuco"),
           MaxRecords = 5,
           Model = "Coords")
           
## End(Not run)

diogosbr/splink documentation built on Jan. 19, 2024, 5:15 p.m.