| Title: | Access the Global Plant Phenology Data Portal |
|---|---|
| Description: | Search plant phenology data aggregated from several sources and available on the Global Plant Phenology Data Portal. |
| Authors: | John Deck [aut, cre], Brian Stucky [aut], Ramona Walls [aut], Kjell Bolmgren [aut], Ellen Denny [aut], Dubois Salix [aut], Ellen Denny [aut], Robert Guralnick [aut] |
| Maintainer: | John Deck <[email protected]> |
| License: | GPL-2 |
| Version: | 2.0 |
| Built: | 2024-08-23 05:33:04 UTC |
| Source: | https://github.com/ropensci/rppo |
Access data from the global plant phenology data portal (PPO data portal) and phenology terms from the Plant Phenology Ontology (PPO)
rppo enables users to query the global plant phenology data portal (PPO data portal). The PPO data portal is an aggregation of phenology data from several different data sources. Currently it contains USA-NPN, NEON, and PEP725 data sources. The PPO data portal harvests data using the ppo-data-pipeline, with code available at https://github.com/biocodellc/ppo-data-pipeline/. All phenological terms in the data portal are aligned using the Plant Phenology Ontology (PPO), available at https://github.com/PlantPhenoOntology/ppo.
Three main functions are contained in the rppo:
ppo_terms allows users to discover present and absent
phenological stages, ppo_data enables users to query the
PPO data portal and ppo_traits use the data fetched from the
PPO data portal and return the traits data for each eventID.
The rppo package source code is available at
https://github.com/ropensci/rppo/.
Maintainer: John Deck [email protected]
Authors:
Brian Stucky [email protected]
Ramona Walls [email protected]
Kjell Bolmgren [email protected]
Ellen Denny [email protected]
Dubois Salix [email protected]
Ellen Denny [email protected]
Robert Guralnick [email protected]
Useful links:
Report bugs at https://github.com/ropensci/rppo/issues
Access data from the global plant phenology data portal (PPO data portal)
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 )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 )
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
|
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/). |
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.
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
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)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)
ppo_data.A list of the sources, sub-sources, status, traits and genera available and their number of observations in the PPO data portal.
ppo_filtersppo_filters
A list with 5 element:
sourceA data set with 1 row and 2 variable:
sourcethe source name
nObsthe number of obeservations
subSourceA data set with 1 row and 2 variable:
subSourcethe subSource name
nObsthe number of obeservations
statusA data set with 1 row and 2 variable:
statusthe status name
nObsthe number of obeservations
mapped_traitsA data set with 1 row and 2 variable:
termIDthe term ID
labelthe term label
definitionthe term definition from Ontobee
urithe link to the term page from Ontobee
nObsthe number of obeservations
statusif the term status is 'present' or 'absent; useful to filter by status
ObjectProperty_termIDthe term for an object propriety in the definition; useful to filter for similar terms
ObjectProperty_termID1the term for a second object propriety in the definition; useful to filter for similar terms
ObjectProperty_termID2the term for a third object propriety in the definition; useful to filter for similar terms
...
Access present and absent terms from the Plant Phenology Ontology
ppo_get_terms(present = FALSE, absent = FALSE)ppo_get_terms(present = FALSE, absent = FALSE)
present |
(boolean) If TRUE then return all "present" phenological stages |
absent |
(boolean) IF TRUE then return all "absent" phenological stages. |
The ppo_terms function returns terms from the Plant Phenology Ontology (PPO).
The termID or label column can be used to query the 'termID' or
'mapped_traits' to ppo_data. The label and description
columns are useful in determining the trait to query on. The URI column
contains a link to the term itself which is useful for determining superclass
and subclass relationships for each term.
A data frame with the columns: termID, label, description, and URI.
presentTerms <- ppo_terms(present = TRUE) absentTerms <- ppo_terms(absent = TRUE) allTerms <- ppo_terms(present = TRUE, absent = TRUE) fruitTerms <- grep("fruit", ppo_filters$mapped_traits$label, value = TRUE) ppo_data(genus = c( "Pinus", "Quercus"), specificEpithet = "palustris", mapped_traits = fruitTerms, fromYear = 2016, toYear = 2017)presentTerms <- ppo_terms(present = TRUE) absentTerms <- ppo_terms(absent = TRUE) allTerms <- ppo_terms(present = TRUE, absent = TRUE) fruitTerms <- grep("fruit", ppo_filters$mapped_traits$label, value = TRUE) ppo_data(genus = c( "Pinus", "Quercus"), specificEpithet = "palustris", mapped_traits = fruitTerms, fromYear = 2016, toYear = 2017)
Access present and absent terms from the Plant Phenology Ontology
ppo_terms(present = FALSE, absent = FALSE, timeLimit = 4)ppo_terms(present = FALSE, absent = FALSE, timeLimit = 4)
present |
(boolean) If TRUE then return all "present" phenological stages |
absent |
(boolean) IF TRUE then return all "absent" phenological stages. |
timeLimit |
(integer) set the limit of the amount of time to wait for a response |
The ppo_terms function returns terms from the Plant Phenology Ontology (PPO).
The function only accepts parameters for "present" or "absent" terms.
The response populates a data frame with: termID, label, description, and
URI. Use the termID values in submitting termID values to the
ppo_data function. The label and description fields are
extracted from the Plant Phenology Ontology and are useful in
determining the proper term to query on. The URI field contains a link to
the term itself which is useful for determining superclass and subclass
relationships for each term.
Some of these terms will not return any results when using
ppo_data.
To have only the ones that will return results, use ppo_get_terms
or check rppo:::ppo_filters$mapped_traits which contains both present
and absent terms.
For more information on the PPO ontology itself, we suggest loading the PPO
https://github.com/PlantPhenoOntology/ppo with
protege https://protege.stanford.edu/
data.frame
presentTerms <- ppo_terms(present = TRUE, timeLimit = 1) absentTerms <- ppo_terms(absent = TRUE, timeLimit = 1)presentTerms <- ppo_terms(present = TRUE, timeLimit = 1) absentTerms <- ppo_terms(absent = TRUE, timeLimit = 1)
Get the traits data from the [ppo_data()] event ids.
ppo_traits(x, sorted = TRUE, flatten_traits = TRUE, flatten_all = FALSE)ppo_traits(x, sorted = TRUE, flatten_traits = TRUE, flatten_all = FALSE)
x |
(object) As returned from link(rppo)[ppo_data] |
sorted |
(logical) Should the output traits be sorted by category. Default : TRUE |
flatten_traits |
(logical) Should the traits list be melted in a data.frame. Default : TRUE |
flatten_all |
(logical) Should the output list be melted in a data.frame. Default : FALSE |
If sorted is TRUE, a list for each event id containing a list with the following elements:
'metadata': A data frame containing metadata
'taxonomy': A data.frame containing the taxonomy
'traits': if flatten_traits is TRUE, a melted data.frame, else a list containing the traits value
Else, a list of data.frames for each event id. IF flatten_all is TRUE, the list is flatten to a data.frame
r1 <- ppo_data(genus = "Quercus", termID='obo:PPO_0002313', limit=10, timeLimit = 4) r1_traits <- ppo_traits(r1)r1 <- ppo_data(genus = "Quercus", termID='obo:PPO_0002313', limit=10, timeLimit = 4) r1_traits <- ppo_traits(r1)
Turn the traits element or the entire list returned by [pp_traits()] into a data.frame.
ppo_traits_flatten(x, flatten_all = FALSE)ppo_traits_flatten(x, flatten_all = FALSE)
x |
(object) A list or data.frame as returned from link(rppo)[ppo_traits] |
flatten_all |
(logical) Should the output list be melted in a data.frame. Default : FALSE |
A list for each event id containing a list with the following elements:
'metadata': A data frame containing metadata
'taxonomy': A data.frame containing the taxonomy
'traits': A melted data.frame containing the traits value
IF flatten_all is TRUE, the list is flatten to a data.frame
r1 <- ppo_data(genus = "Quercus", termID = 'obo:PPO_0002313', limit = 10, timeLimit = 4) r1_traits <- ppo_traits(r1, sorted = FALSE, flatten_traits = FALSE) r1_traits <- ppo_traits_flatten(r1_traits, flatten_all = TRUE)r1 <- ppo_data(genus = "Quercus", termID = 'obo:PPO_0002313', limit = 10, timeLimit = 4) r1_traits <- ppo_traits(r1, sorted = FALSE, flatten_traits = FALSE) r1_traits <- ppo_traits_flatten(r1_traits, flatten_all = TRUE)
Title
ppo_traits_sort(x, flatten_traits = TRUE, flatten_all = FALSE)ppo_traits_sort(x, flatten_traits = TRUE, flatten_all = FALSE)
x |
(object) A list or data.frame as returned from link(rppo)[ppo_traits] with sorted set to FALSE. |
flatten_traits |
(logical) Should the traits list be melted in a data.frame. Default : TRUE |
flatten_all |
(logical) Should the output list be melted in a data.frame. Default : FALSE |
A list for each event id containing a list with the following elements:
'metadata': A data frame containing metadata
'taxonomy': A data.frame containing the taxonomy
'traits': if flatten_traits is TRUE, a melted data.frame, else a list containing the traits value
IF flatten_all is TRUE, the list is flatten to a data.frame
r1 <- ppo_data(genus = "Quercus", termID='obo:PPO_0002313', limit=10, timeLimit = 4) r1_traits <- ppo_traits(r1, sorted = FALSE) r1_traits <- ppo_traits_sort(r1_traits)r1 <- ppo_data(genus = "Quercus", termID='obo:PPO_0002313', limit=10, timeLimit = 4) r1_traits <- ppo_traits(r1, sorted = FALSE) r1_traits <- ppo_traits_sort(r1_traits)