ppo_data: Access Data From the Global Plant Phenology Data Portal
In biocodellc/rppo: Access the Global Plant Phenology Data Portal

View source: R/ppo_data.R

ppo_data

R Documentation

Access Data From the Global Plant Phenology Data Portal

Description

Access data from the global plant phenology data portal (PPO data portal)

Usage

ppo_data(
  scientificName = NULL,
  genus = NULL,
  specificEpithet = NULL,
  termID = NULL,
  fromYear = NULL,
  toYear = NULL,
  fromDay = NULL,
  toDay = NULL,
  bbox = NULL,
  source = NULL,
  subSource = NULL,
  status = NULL,
  mapped_traits = NULL,
  eventRemarks = NULL,
  limit = 100000L,
  timeLimit = 60,
  keepData = FALSE
)

Arguments

`scientificName`	(character) A plant species scientific name.
`genus`	(character) A plant genus name. See details.
`specificEpithet`	(character) A plant specific epithet
`termID`	(character) A single termID from the plant phenology ontology. See details.
`fromYear`	(integer) return data from the specified year
`toYear`	(integer) return data up to and including the specified year
`fromDay`	(integer) return data starting from the specified day
`toDay`	(integer) return data up to and including the specified day
`bbox`	(character) return data within a bounding box. Format is `lat,long,lat,long` and is structured as a string. Use this website: http://boundingbox.klokantech.com/ to quickly grab a bbox (set format on bottom left to csv and be sure to switch the order from long, lat, long, lat to lat, long, lat, long).
`source`	(character) return data from specified source. See details.
`subSource`	(character) return data from the specified sub-source. See details.
`status`	(character) Either "present" or "absent". Return data with the specified status.
`mapped_traits`	(character) return data from the specified traits. See details
`eventRemarks`	(character) return data from the specified eventRemarks
`limit`	(integer) limit returned data to a specified number of records
`timeLimit`	(integer) set the limit of the amount of time to wait for a response
`keepData`	(logical) whether to keep (TRUE) or delete (FALSE; default) the downloaded data (~/ppo_download/).

Details

The ppo_data function returns a list containing the following information: a readme file, citation information, a data frame with data, an integer with the number of records returned and a status code. The function is called with parameters that correspond to values contained in the data itself which act as a filter on the returned record set. For a list of available mapped_traits, termID, Source and subSource see the ppo_filters dataset. For mapped_traits and termID, the ppo_get_terms function will return a data.frame with present, absent or both terms and traits information. The ppo_terms will do the same but will use the API to get the lastest data. However, some of the traits/termID may not return any results from this function. See their documentation for more details.

Value

A list with the following elements:

'data': A data frame containing data
'readme': A string with information about the return package
'citation': A string with citation information
'number_possible': An integer with total possible results
'status_code': An integer with status code returned from server

Examples


r1 <- ppo_data(genus = c("Quercus", "Pinus"), termID='obo:PPO_0002313',
limit=10, timeLimit = 4)
head(r1$data)

r2 <- ppo_data(fromDay = 1, toDay = 100, bbox="37,-120,38,-119", limit=10,
timeLimit = 4)
head(r2$data)

biocodellc/rppo documentation built on July 8, 2023, 12:45 p.m.