npn_download_site_phenometrics {rnpn}

Download Site Phenometrics

Description

This function allows for a parameterized search of all site phenometrics records in the USA-NPN database, returning all records as per the search parameters 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 converted to CSV and 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.

Usage

npn_download_site_phenometrics(
  request_source,
  years,
  num_days_quality_filter = "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,
  six_leaf_layer = FALSE,
  six_bloom_layer = FALSE,
  agdd_layer = NULL,
  six_sub_model = NULL,
  additional_layers = NULL,
  taxonomy_aggregate = NULL,
  pheno_class_aggregate = NULL,
  wkt = NULL
)

Arguments

request_source

Required field, string. Self-identify who is making requests to the data service

years

Required field, list of strings. Specify the years to include in the search, e.g. c('2013','2014'). You must specify at least one year.

num_days_quality_filter

Required field, defaults to 30. The integer value sets the upper limit on the number of days difference between the first Y value and the previous N value for each individual to be included in the data aggregation.

coords

List of float values, 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 )

species_ids

List of unique IDs for searching based on species, e.g. c ( 3, 34, 35 )

genus_ids

List 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.

family_ids

List 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.

order_ids

List 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.

class_ids

List 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.

pheno_class_ids

List of unique IDs for searching based on pheno class id, e.g. c (1, 5, 13)

station_ids

List of unique IDs for searching based on site location, e.g. c ( 5, 9, ... )

species_types

List of unique species type names for searching based on species types, e.g. c ( "Deciduous", "Evergreen" )

network_ids

List of unique IDs for searching based on partner group/network, e.g. ( 500, 300, ... )

states

List of US postal states to be used as search params, e.g. c ( "AZ", "IL" )

phenophase_ids

List of unique IDs for searching based on phenophase, e.g. c ( 323, 324, ... )

functional_types

List of unique functional type names, e.g. c ( "Birds" )

additional_fields

List of additional fields to be included in the search results, e.g. ( "Station_Name", "Plant_Nickname" )

climate_data

Boolean value indicating that all climate variables should be included in additional_fields

ip_address

Optional field, string. IP Address of user requesting data. Used for generating data reports

dataset_ids

List of unique IDs for searching based on dataset, e.g. NEON or GRSM c(17,15)

email

Optional field, string. Email of user requesting data.

download_path

Optional file path to which search results should be re-directed for later use.

six_leaf_layer

Boolean value when set to true will attempt to resolve the date of the observation to a spring index, leafing value for the location at which the observations was taken

six_bloom_layer

Boolean value when set to true will attempt to resolve the date of the observation to a spring index, bloom value for the location at which the observations was taken

agdd_layer

numeric value, accepts 32 or 50. When set, the results will attempt to resolve the date of the observation to an AGDD value for the location; the 32 or 50 represents the base value of the AGDD value returned. All AGDD values are based on a January 1st start date of the year in which the observation was taken.

six_sub_model

Affects the results of the six layers returned. Can be used to specify one of three submodels used to calculate the spring index values. Thus setting this field will change the results of six_leaf_layer and six_bloom_layer. Valid values include: 'lilac','zabelli' and 'arnoldred'. For more information see the NPN's Spring Index Maps documentation: https://www.usanpn.org/data/spring_indices

additional_layers

Data frame with first column named 'name' and containing the names of the layer for which to retrieve data and the second column named 'param' and containing string representations of the time/elevation subset parameter to use. This variable can be used to append additional geospatial layer data fields to the results, such that the date of observation in each row will resolve to a value from the specified layers, given the location of the observation.

taxonomy_aggregate

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.

pheno_class_aggregate

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

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.

Details

This data type includes estimates of the overall onset and end of phenophase activity for plant and animal species at a site over a user-defined time period. Each row provides the first and last occurrences of a given phenophase on a given species, beginning with the date of the first observed "yes" phenophase status record and ending with the date of the last observed "yes" record of the user-defined time period. For plant species where multiple individuals are monitored at the site, the date provided for "first yes" is the mean of the first "yes" records for each individual plant at the site, and the date for "last yes" is the mean of the last "yes" records. Note that a phenophase may have ended and restarted during the overall period of its activity at the site. These more fine-scale patterns can be explored in the individual phenometrics data.

Most search parameters are optional, however, users are encouraged to supply additional search parameters to get results that are easier to work with. 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 additional, 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 https://docs.google.com/document/d/1yNjupricKOAXn6tY1sI7-EwkcfwdGUZ7lxYv7fcPjO8/edit#heading=h.ueaexz9bczti Metadata on all fields can be found in the following Excel sheet: http://www.usanpn.org/files/metadata/site_phenometrics_datafield_descriptions.xlsx

Value

Data table of all status records returned as per the search parameters. Null if output directed to file.

Examples

## Not run: 
#Download all saguaro data for 2013 and 2014
npn_download_site_phenometrics(
  request_source="Your Name or Org Here",
  years=c('2013','2014'),
  species_id=c(210),
  download_path="saguaro_data_2013_2014.json"
)

## End(Not run)