In cadubio/splinkr: Connect R environment to speciesLink network

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splinkr

The purpose of this package is to connect R environment to speciesLink, a collaborative network that includes the participation of hundreds of biological collections in Brazil and abroad, whose main objective is to give access to anyone interested in the data about the records held by collections, and observation data (cria.org.br).

This package uses CRIA speciesLink API v.0.1 beta (CRIA) as source of the data and the Exsiccatae service (INCT-HVFF) as images source.

Installation

You can install the released version of splinkr from GitHub with:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("cadubio/splinkr")

Usage

There are tree functions in package: splinkr_datasets, splinkr_records and splinkr_images.

# load package
library(splinkr)

Function splinkr_datasets()

The function splinkr_datasets() with no arguments returns a tibble with all datasets of biological collections included in speciesLink network.

splinkr_datasets()

Pass one term to filter argument filtering all variables (columns) of datasets.

splinkr_datasets(filter = "universidade")

If more than one term is passed to filter, intersection filtering is performed, that is, the search with second term is only performed on subset obtained from filtering with first term. The search with third term is only done in subset of second term and so on...

splinkr_datasets(filter = c("universidade", "herbário", "brasil"))

Note that filtering do not matches case, but matches with portuguese diacritical signs.

splinkr_datasets(filter = c("Herbario"))

splinkr_datasets(filter = c("herbário"))

Function splinkr_records()

This is the main function of the package. It provides a search engine for the more than 14 million speciesLink records. All arguments are NULL by default. Arguments scientificName, barcode and catalogNumber are mutualy excludent, on the other hand, one of the them can mixed with all other arguments. See list of arguments below.

| Argument | Options | Example | | ---------|-------------------|----------------------------------------------| | barcode | character vector | c("NY00000001", "FPS00257", "FCM00096") | | basisOfRecord | PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation, MaterialSample | c("PreservedSpecimen") | | collectionCode | character vector | c("FIOCRUZ-CEIOC", "UEC", "HUEFS") | | catalogNumber | character vector, embranco, nãobranco | c("435643", "P234576", "embranco) | | collector | collector name | c("Siqueira", "Almeida F") | | collectorNumber | character vector | c("125", "1897A") | | yearCollected | four-digits year | c(1887, 1897, 2000)| | identifiedBy | character vector | c("Siqueira CE")| | yearIdentified | four-digits year | c(1997, 2015)| | kingdom | character vector | c("Plantae", "Animalia", "Fungi")| | phylum | character vector | c("Arthropoda", "Nematoda") | | class | character vector | c("Reptilia", "Amphibia")| | order | character vector | c("Crocodilia", "Anura") | | family | character vector | c("Bromeliaceae", "Apidae") | | genus | character vector | c("Tabebuia", "Bacillus", "Hoplias") | | scientificName | character vector | c("Bothrops neuwiedii matogrossensis", "Leishmania braziliensis") | | typus | NULL, yes | "yes" | | country | character vector | c("Brasil", "Argentina") | | stateProvince | character vector | c("SP", "Santa Catarina", "MT") | | county | character vector | c("São José", "Anitápolis", "Rio Branco") | | locality | character vector | c("pedra branca", "fazendinha") | | maxRecords | character vector | "5" |
| redlist | NULL, yes | "yes" |

Code examples

# scientific name query 
splinkr_records(scientificName = "Dyckia encholirioides var. rubra")


splinkr_records(scientificName = c("Acianthera saundersiana", "Anathallis microphyta"),
                collector = "Siqueira")

# Returns only type species
splinkr_records(scientificName = c("Campylocentrum insulare", "Acianthera saundersiana"), collectionCode = "FLOR", typus = "yes")

A large number of scientific names may be passed but the return may take a while, so it possible limit the number of records to return with maxrecords argument

# Vector names
nomes <- c("Abarema turbinata", "Comolia villosa", "Stylosanthes campestris", 
"Vochysia floribunda", "Eugenia platyphylla", "Chaetocalyx acutifolia", 
"Actinocephalus ochrocephalus", "Cicuta douglasii", "Annona senegalensis", 
"Hexasepalum radula", "Trichosalpinx dura", "Allophylus sericeus", 
"Microlicia juniperina", "Campomanesia pubescens", "Luxemburgia ciliosa", 
"Dalechampia humilis", "Croton heliotropiifolius", "Senna alata", 
"Ipomoea dichotoma", "Arundo donax")

# Note that maxrecords must be passed as a character (quoted number)
splinkr_records(scientificName = nomes, maxrecords = "20")

Function splinkr_images()

The goal of this function is to provide a relatively quick way to view images of collections. According (cria.org.br) there are more than three million records with images. Package imager is used to display this images.

In the future an integration with imageJ may be provided to download and examine images from specimen records.

# Display image by `imagecode`
splinkr_images(imagecode = c("FLOR0037759", "UEC190851", "FURB53840"))

# Display image by `scientificName`
splinkr_images(scientificName = c("Spigelia insignis", "Anathallis kleinii"))

knitr::include_graphics('images/imager-display.png')

knitr::include_graphics('images/imager-showimage.png')

Using pipe

The results of splinkr_records can be passed via %>% (pipe) to splinkr_images to display images.

# View images of genus 'Campylocentrum' from UPCB herbarium
splinkr_records(scientificName = "Campylocentrum", collectionCode = "UPCB") %>% 
  splinkr_images(imagecode = .)

Data and image sources

CRIA, Centro de Referência em Informação Ambiental. speciesLink API v.0.1 beta. (api.splink.org.br), accessed 5.10.2020.

INCT-HVFF, Herbário Virtual da Flora e dos Fungos. (reflora-cdc.cria.org.br/inct/exsiccatae), accessed 5.10.2020.

Packages used in this project

Duncan Temple Lang (2020). XML: Tools for Parsing and Generating XML Within R and S-Plus. R package version 3.99-0.5. (CRAN)

Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2020). dplyr: A Grammar of Data Manipulation. R package version 1.0.2. (CRAN)

Hadley Wickham, Jim Hester and Jeroen Ooms (2020). xml2: Parse XML. R package version 1.3.2. (CRAN)

Kirill Müller and Hadley Wickham (2020). tibble: Simple Data Frames. R package version 3.0.3. (CRAN)

Lionel Henry and Hadley Wickham (2020). purrr: Functional Programming Tools. R package version 0.3.4. (CRAN)

Simon Barthelme (2020). imager: Image Processing Library Based on 'CImg'. R package version 0.42.3. (CRAN)

Stefan Milton Bache and Hadley Wickham (2014). magrittr: A Forward-Pipe Operator for R. R package version 1.5. (CRAN)

cadubio/splinkr documentation built on Oct. 13, 2020, 8:36 p.m.