R/npn_data_download.R
npn_download_magnitude_phenometrics.RdThis function allows for a parameterized search of all magnitude phenometrics in the USA-NPN database, returning all records as per the search results in a data table. Data fetched from NPN services is returned as raw JSON before being channeled into a data table. Optionally results can be directed to an output file in which case raw JSON is saved to file; in that case, data is also streamed to file which allows for more easily handling of the data if the search otherwise returns more data than can be handled at once in memory.
npn_download_magnitude_phenometrics(
request_source,
years,
period_frequency = "30",
coords = NULL,
species_ids = NULL,
genus_ids = NULL,
family_ids = NULL,
order_ids = NULL,
class_ids = NULL,
pheno_class_ids = NULL,
station_ids = NULL,
species_types = NULL,
network_ids = NULL,
states = NULL,
phenophase_ids = NULL,
functional_types = NULL,
additional_fields = NULL,
climate_data = FALSE,
ip_address = NULL,
dataset_ids = NULL,
email = NULL,
download_path = NULL,
taxonomy_aggregate = NULL,
pheno_class_aggregate = NULL,
wkt = NULL
)Required field, character Self-identify who is making requests to the data service.
Required field, character vector. Specify the years to include
in the search, e.g. c('2013','2014'). You must specify at least one year.
Required field, integer. The integer value specifies
the number of days by which to delineate the period of time specified by
the start_date and end_date, i.e. a value of 7 will delineate the period of
time weekly. Any remainder days are grouped into the final delineation.
This parameter, while typically an int, also allows for a "special" string
value, "months" to be passed in. Specifying this parameter as "months" will
delineate the period of time by the calendar months regardless of how many
days are in each month. Defaults to 30 if omitted.
Numeric vector, used to specify a bounding box as a search
parameter, e.g. c(lower_left_lat, lower_left_long, upper_right, lat,upper_right_long).
Integer vector of unique IDs for searching based on
species, e.g. c(3, 34, 35).
Integer vector of unique IDs for searching based on
taxonomic family, e.g. c(3, 34, 35). This parameter will take precedence
if species_ids is also set.
Integer vector of unique IDs for searching based on
taxonomic family, e.g. c(3, 34, 35). This parameter will take precedence
if species_ids is also set.
Integer vector of unique IDs for searching based on
taxonomic order, e.g. c(3, 34, 35). This parameter will take precedence
if species_ids or family_ids are also set.
Integer vector of unique IDs for searching based on
taxonomic class, e.g. c(3, 34, 35). This parameter will take precedence
if species_ids, family_ids or order_ids are also set.
Integer vector of unique IDs for searching based on
pheno class. Note that if both pheno_class_id and phenophase_id are
provided in the same request, phenophase_id will be ignored.
Integer vector of unique IDs for searching based on site
location, e.g. c(5, 9).
Character vector of unique species type names for
searching based on species types, e.g. c("Deciduous", "Evergreen").
Integer vector of unique IDs for searching based on
partner group/network, e.g. c(500, 300).
Character vector of US postal states to be used as search
params, e.g. c("AZ", "IL").
Integer vector of unique IDs for searching based on
phenophase, e.g. c(323, 324).
Character vector of unique functional type names, e.g. `c("Birds").
Character vector of additional fields to be included
in the search results, e.g. c("Station_Name", "Plant_Nickname").
Boolean value indicating that all climate variables
should be included in additional_fields.
Optional field, string. IP Address of user requesting data. Used for generating data reports.
Integer vector of unique IDs for searching based on
dataset, e.g. NEON or GRSM c(17,15).
Optional field, string. Email of user requesting data.
Character, optional file path to the file for which to output the results.
Boolean value indicating whether to aggregate data
by a taxonomic order higher than species. This will be based on the values
set in family_ids, order_ids, or class_ids. If one of those three
fields are not set, then this value is ignored.
Boolean value indicating whether to aggregate
data by the pheno class ids as per the pheno_class_ids parameter. If the
pheno_class_ids value is not set, then this parameter is ignored. This
can be used in conjunction with taxonomy_aggregate and higher taxonomic
level data filtering.
WKT geometry by which filter data. Specifying a valid WKT within the contiguous US will filter data based on the locations which fall within that WKT.
Data table of all status records returned as per the search
parameters. NULL if output directed to file.
This data type includes various measures of the extent to which a phenophase for a plant or animal species is expressed across multiple individuals and sites over a user-selected set of time intervals. Each row provides up to eight calculated measures summarized weekly, bi-weekly, monthly or over a custom time interval. These measures include approaches to evaluate the shape of an annual activity curve, including the total number of "yes" records and the proportion of "yes" records relative to the total number of status records over the course of a calendar year for a region of interest. They also include several approaches for standardizing animal abundances by observer effort over time and space (e.g. mean active bird individuals per hour). See the Metadata window for more information.
Most search parameters are optional, however, failing to provide even a single search parameter will return all results in the database. Request_Source must be provided. This is a self-identifying string, telling the service who is asking for the data or from where the request is being made. It is recommended you provide your name or organization name. If the call to this function is acting as an intermediary for a client, then you may also optionally provide a user email and/or IP address for usage data reporting later.
Additional fields provides the ability to specify more, non-critical fields to include in the search results. A complete list of additional fields can be found in the NPN service's companion documentation. Metadata on all fields can be found in the following Excel sheet: http://www.usanpn.org/files/metadata/magnitude_phenometrics_datafield_descriptions.xlsx