Title:	Interface to the National 'Phenology' Network 'API'
Version:	1.4.0
Description:	Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (https://usanpn.org/), which includes data on various life history events that occur at specific times.
License:	MIT + file LICENSE
URL:	https://github.com/usa-npn/rnpn, http://usa-npn.github.io/rnpn/
BugReports:	https://github.com/usa-npn/rnpn/issues
Depends:	R (≥ 3.5.0)
Imports:	dplyr, httr2 (≥ 1.1.0), jsonlite, lifecycle, magrittr, rlang, tibble, tidyr, xml2
Suggests:	covr, ggplot2, knitr, markdown, RColorBrewer, rmarkdown, sf, terra, testthat (≥ 3.0.0), vcr, withr
VignetteBuilder:	knitr
Config/testthat/edition:	3
Encoding:	UTF-8
RoxygenNote:	7.3.2
NeedsCompilation:	no
Packaged:	2025-03-25 20:43:55 UTC; jeff
Author:	Jeff Switzer [aut, cre], Scott Chamberlain [aut], Lee Marsh [aut], Kevin Wong [aut], Eric R Scott [aut], David LeBauer [ctb]
Maintainer:	Jeff Switzer <jeff@usanpn.org>
Repository:	CRAN
Date/Publication:	2025-03-25 21:00:05 UTC

Interface to the National Phenology Network API

Description

This package allows for easy access to the National Phenology Network's Data API. To learn more, take a look at the vignettes.

Author(s)

Maintainer: Jeff Switzer jeff@usanpn.org

Authors:

• Scott Chamberlain

• Lee Marsh

• Kevin Wong

• Eric R Scott (ORCID)

Other contributors:

• David LeBauer [contributor]

See Also

Useful links:

• https://github.com/usa-npn/rnpn

• http://usa-npn.github.io/rnpn/

• Report bugs at https://github.com/usa-npn/rnpn/issues

Get Additional Layers

Description

Utility function to easily take arbitrary layer name parameters as a data frame and return the raster data from NPN Geospatial data services.

Usage

get_additional_rasters(data)

Arguments

Value

Returns a data frame containing the raster objects related to the specified layers.

Get Abundance Categories

Description

Gets data on all abundance/intensity categories and includes a data frame of applicable abundance/intensity values for each category

Usage

npn_abundance_categories(...)

Arguments

Value

A data frame listing all abundance/intensity categories and their corresponding values.

Examples

## Not run: 
ac <- npn_abundance_categories()

## End(Not run)

This function is defunct.

Description

This function is defunct.

Usage

npn_allobssp(...)

Check Point Cached

Description

Checks in the global variable "point values" to see if the exact data point being requested has already been asked for and returns the value if it's already saved.

Usage

npn_check_point_cached(layer, lat, long, date)

Arguments

Value

The numeric value of the cell located at the specified coordinates and date if the value has been queried, otherwise NULL.

Get Datasets

Description

Returns a complete list of information about all datasets integrated into the NPN dataset. Data can then be pulled for individual datasets using their unique IDs.

Usage

npn_datasets(...)

Arguments

Value

tibble of datasets and their IDs.

Examples

## Not run: 
npn_datasets()

## End(Not run)

Download Geospatial Data

Description

Function for directly downloading any arbitrary Geospatial layer data from the NPN Geospatial web services.

Usage

npn_download_geospatial(
  coverage_id,
  date,
  format = "geotiff",
  output_path = NULL
)

Arguments

Details

Information about the layers can also be viewed at the getCapbilities page directly: https://geoserver.usanpn.org/geoserver/wms?request=GetCapabilities

Value

returns nothing when output_path is set, otherwise a terra::SpatRaster object meeting the coverage_id, date and format parameters specified.

Examples

## Not run: 
ras <- npn_download_geospatial("si-x:30yr_avg_six_bloom", "255")

## End(Not run)

Download Individual Phenometrics

Description

This function allows for a parameterized search of all individual 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_individual_phenometrics(
  request_source,
  years,
  period_start = "01-01",
  period_end = "12-31",
  coords = NULL,
  individual_ids = NULL,
  species_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,
  genus_ids = NULL,
  family_ids = NULL,
  order_ids = NULL,
  class_ids = NULL,
  pheno_class_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,
  wkt = NULL
)

Arguments

Details

This data type includes estimates of the dates of phenophase onsets and ends for individual plants and for animal species at a site during a user-defined time period. Each row represents a series of consecutive "yes" phenophase status records, beginning with the date of the first "yes" and ending with the date of the last "yes", submitted for a given phenophase on a given organism. Note that more than one consecutive series for an organism may be present within a single growing season or year.

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 Metadata on all fields can be found in the following Excel sheet: https://www.usanpn.org/files/metadata/individual_phenometrics_datafield_descriptions.xlsx

Value

A tibble of all status records returned as per the search parameters. If download_path is specified, the file path is returned instead.

Examples

## Not run: 
#Download all saguaro data for 2013 and 2014 using "water year" as the period
npn_download_individual_phenometrics(
  request_source = "Your Name or Org Here",
  years = c(2013, 2014),
  period_start = "10-01",
  period_end = "09-30",
  species_id = 210,
  download_path = "saguaro_data_2013_2014.csv"
)

## End(Not run)

Download Magnitude Phenometrics

Description

This 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.

Usage

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
)

Arguments

Details

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: https://www.usanpn.org/files/metadata/magnitude_phenometrics_datafield_descriptions.xlsx

Value

A tibble of the requested data. If a download_path was specified, the file path is returned.

Examples

## Not run: 
#Download book all saguaro data for 2013
npn_download_magnitude_phenometrics(
  request_source="Your Name or Org Here",
  years=c(2013),
  species_id=c(210),
  download_path="saguaro_data_2013.csv"
)

## End(Not run)

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,
  period_start = "01-01",
  period_end = "12-31",
  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

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. Metadata on all fields can be found in the following Excel sheet: https://www.usanpn.org/files/metadata/site_phenometrics_datafield_descriptions.xlsx

Value

A tibble of all status records returned as per the search parameters. If download_path is specified, the file path is returned instead.

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 = 210,
  download_path = "saguaro_data_2013_2014.csv"
)

## End(Not run)

Download Status and Intensity Records

Description

This function allows for a parameterized search of all status 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 the 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_status_data(
  request_source,
  years,
  coords = NULL,
  species_ids = NULL,
  genus_ids = NULL,
  family_ids = NULL,
  order_ids = NULL,
  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,
  pheno_class_ids = NULL,
  wkt = NULL
)

Arguments

Details

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 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: https://www.usanpn.org/files/metadata/status_intensity_datafield_descriptions.xlsx

Value

A tibble of all status records returned as per the search parameters. If download_path is specified, the file path is returned instead.

Examples

## Not run: 
#Download all saguaro data for 2016
npn_download_status_data(
  request_source = "Your Name or Org Here",
  years = c(2016),
  species_id = c(210),
  download_path = "saguaro_data_2016.csv"
)

## End(Not run)

Get AGDD Point Value

Description

This function is for requesting AGDD point values. Because the NPN has a separate data service that can provide AGDD values which is more accurate than Geoserver this function is ideal when requested AGDD point values.

Usage

npn_get_agdd_point_data(layer, lat, long, date, store_data = TRUE)

Arguments

Details

As this function only works for AGDD point values, if it's necessary to retrieve point values for other layers please try the npn_get_point_data() function.

Value

Returns a numeric value of the AGDD value at the specified lat/long/date. If no value can be retrieved, then -9999 is returned.

Examples

## Not run: 
npn_get_agdd_point_data(
  layer = "gdd:agdd",
  lat = 32.4,
  long = -110,
  date = "2020-01-15"
)

## End(Not run)

Get Common Query String Variables

Description

Utility function to generate a list of query string variables for requests to NPN data service points. Some parameters are basically present in all requests, so this function helps put them together.

Usage

npn_get_common_query_vars(
  request_source,
  coords = NULL,
  species_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,
  genus_ids = NULL,
  family_ids = NULL,
  order_ids = NULL,
  class_ids = NULL,
  pheno_class_ids = NULL,
  taxonomy_aggregate = NULL,
  pheno_class_aggregate = NULL,
  wkt = NULL,
  email = NULL
)

Value

List of query string variables.

Get Custom AGDD Raster Map

Description

This function takes a series of variables used in calculating AGDD and returns a raster of the continental USA with each pixel representing the calculated AGDD value based on start and end date. This function leverages the USA-NPN geo web services.

Usage

npn_get_custom_agdd_raster(
  method,
  climate_data_source,
  temp_unit,
  start_date,
  end_date,
  base_temp,
  upper_threshold = NULL
)

Arguments

Value

A terra::SpatRaster object of each calculated AGDD numeric values based on specified time period/method/base temp/data source.

Examples

## Not run: 
res <- npn_get_custom_agdd_raster(
  method = "simple",
  climate_data_source = "NCEP",
  temp_unit = "Fahrenheit",
  start_date = "2020-01-01",
  end_date = "2020-01-15",
  base_temp = 32
)

## End(Not run)

Get Custom AGDD Time Series

Description

This function takes a series of variables used in calculating AGDD and returns an AGDD time series, based on start and end date, for a given location in the continental US. This function leverages the USA-NPN geo web services

Usage

npn_get_custom_agdd_time_series(
  method,
  start_date,
  end_date,
  base_temp,
  climate_data_source,
  temp_unit,
  lat,
  long,
  upper_threshold = NULL
)

Arguments

Value

A data frame containing the numeric AGDD values for each day for the specified time period/location/method/base temp/data source.

Examples

## Not run: 
res <- npn_get_custom_agdd_time_series(
  method = "double-sine",
  start_date = "2019-01-01",
  end_date = "2019-01-15",
  base_temp = 25,
  climate_data_source = "NCEP",
  temp_unit = "fahrenheit",
  lat = 39.7,
  long = -107.5,
  upper_threshold = 90
)

## End(Not run)

Download NPN Data

Description

Generic utility function for querying data from the NPN data services.

Usage

npn_get_data(
  endpoint,
  query,
  download_path = NULL,
  always_append = FALSE,
  six_leaf_raster = NULL,
  six_bloom_raster = NULL,
  agdd_layer = NULL,
  additional_layers = NULL
)

Arguments

Value

A tibble of the requested data. If a download_path was specified, the file path is returned.

Examples

## Not run: 
npn_get_data(
  endpoint = "observations/getObservations.ndjson",
  query = list(
    request_src = "Unit Test",
    climate_data = "0",
    `species_id[1]` = "6",
    start_date = "2010-01-01",
    end_date = "2010-12-31"
  )
)

## End(Not run)

Get Data By Year

Description

Utility function to chain multiple requests to npn_get_data for requests where data should only be retrieved on an annual basis, or otherwise automatically be delineated in some way. Results in a data table that's a combined set of the results from each request to the data service.

Usage

npn_get_data_by_year(
  endpoint,
  query,
  years,
  period_start = "01-01",
  period_end = "12-31",
  download_path = NULL,
  six_leaf_layer = FALSE,
  six_bloom_layer = FALSE,
  agdd_layer = NULL,
  six_sub_model = NULL,
  additional_layers = NULL
)

Arguments

Value

A tibble combining each requests results from the service. If download_path is specified, the file path is returned instead.

Examples

## Not run: 
endpoint <- "/observations/getObservations.json"
query <- list(
  request_src = "Unit%20Test",
  climate_data = "0",
  `species_id[1]` = "6"
)

npn_get_data_by_year(endpoint = endpoint,
                     query = query,
                     years = c(2013, 2014))

#Set a custom period from October through September
# This will return data for 2013-10-01 through 2014-09-30 and from 2014-10-01
# through 2015-09-30
npn_get_data_by_year(
  endpoint = endpoint,
  query = query,
  years = c(2013, 2014),
  period_start = "10-01",
  period_end = "09-30"
)

## End(Not run)

Get Geospatial Data Layer Details

Description

This function will return information about the various data layers available via the NPN's geospatial web services. Specifically, this function will query the NPN's GetCapabilities endpoint and parse the information on that page about the layers. For each layer, this function will retrieve the layer name (as to be specified elsewhere programmatically), the title (human readable), the abstract, which describes the data in the layer, the dimension name and dimension range for specifying specific date values from the layer.

Usage

npn_get_layer_details()

Details

Information about the layers can also be viewed at the getCapbilities page directly: https://geoserver.usanpn.org/geoserver/wms?request=GetCapabilities

Value

A tibble containing all layer details as specified in function description.

Examples

## Not run: 
layers <- npn_get_layer_details()

## End(Not run)

Get Phenophases for Taxon

Description

This function gets a list of phenophases that are applicable for a provided taxonomic grouping, e.g. family, order. Note that since a higher taxononmic order will aggregate individual species not every phenophase returned through this function will be applicable for every species belonging to that taxonomic group.

Usage

npn_get_phenophases_for_taxon(
  family_ids = NULL,
  order_ids = NULL,
  class_ids = NULL,
  genus_ids = NULL,
  date = NULL,
  return_all = 0,
  ...
)

Arguments

Details

It's also important to note that phenophase definitions can change for individual species over time, so there's a need to specify either a date of interest, or to explicitly state that the function should return all phenophases that were ever applicable for any species belonging to the specified taxonomic group.

When called, this function requires of these three parameters, exactly one of family_ids, order_ids or class_ids to be set.

Value

A data frame listing phenophases in the NPN database for the specified taxon and date.

Examples

## Not run: 
npn_get_phenophases_for_taxon(class_ids = c(5, 6), date = "2018-05-05")
npn_get_phenophases_for_taxon(family_ids = c(267, 268), date = "2018-05-05")

#if you supply two or more "ids" arguments, the highest classification takes precedence
pheno <- npn_get_phenophases_for_taxon(
  class_ids = 4,
  family_ids = c(103, 104),
  genus_ids = c(409, 957, 610),
  date = "2018-05-05"
)

colnames(pheno)
# [1] "family_id"   "family_name" "phenophases"

## End(Not run)

Get Point Data Value

Description

This function can get point data about any of the NPN geospatial layers.

Usage

npn_get_point_data(layer, lat, long, date, store_data = TRUE)

Arguments

Details

Please note that this function pulls this from the NPN's WCS service so the data may not be totally precise. If you need precise AGDD values try using the npn_get_agdd_point_data() function.

Value

Returns a numeric value for any NPN geospatial data layer at the specified lat/long/date. If no value can be retrieved, then -9999 is returned.

Examples

## Not run: 
value <-
  npn_get_point_data(
    layer = "gdd:agdd",
    lat = 38.8,
    long = -110.5,
    date = "2022-05-05"
  )

## End(Not run)

Get Partner Groups

Description

Returns a list of all groups participating in the NPN's data collection program. These details can be used to further filter other service endpoints' results.

Usage

npn_groups(use_hierarchy = FALSE, ...)

Arguments

Value

A tibble (or nested list if use_hierarchy = TRUE) of partner groups, including network_id and network_name.

Examples

## Not run: 
npn_groups()
npn_groups(use_heirarchy = TRUE)

## End(Not run)

This function is defunct.

Description

This function is defunct.

Usage

npn_indsatstations(...)

This function is defunct.

Description

This function is defunct.

Usage

npn_indspatstations(...)

Species Name Lookup

Description

Look up species IDs by taxonomic or common name

Usage

npn_lookup_names(name, type = "genus", fuzzy = FALSE)

Arguments

Value

A data frame with species ID numbers based on the name and type parameters.

Examples

## Not run: 
npn_lookup_names(name = 'Pinus', type = 'genus')
npn_lookup_names(name = 'pine', type = 'common_name')
npn_lookup_names(name = 'bird', type = 'common_name', fuzzy = TRUE)

## End(Not run)

Merge Geo Data

Description

Utility function to intersect point based observational data with Geospatial data values. This will take a data frame and append a new column to it.

Usage

npn_merge_geo_data(ras, col_label, df)

Arguments

Value

The data frame, now appended with a new column for geospatial data numeric values.

This function is defunct.

Description

This function is defunct.

Usage

npn_obsspbyday(...)

Get Pheno Classes

Description

Gets information about all pheno classes, which are a higher-level order of phenophases.

Usage

npn_pheno_classes(...)

Arguments

Value

A tibble listing the pheno classes in the NPN database.

Examples

## Not run: 
pc <- npn_pheno_classes()

## End(Not run)

Get Phenophase Definitions

Description

Retrieves a complete list of all phenophase definitions.

Usage

npn_phenophase_definitions(...)

Arguments

Value

A tibble listing all phenophases in the NPN database and their definitions.

Examples

## Not run: 
pp <- npn_phenophase_definitions()

## End(Not run)

Get Phenophase Details

Description

Retrieves additional details for select phenophases, including full list of applicable phenophase definition IDs and phenophase revision notes over time

Usage

npn_phenophase_details(ids = NULL, ...)

Arguments

Value

A tibble listing phenophases in the NPN database, including detailed information for each, filtered by the phenophase ID.

Examples

## Not run: 
pd <- npn_phenophase_details(c(56, 57))

## End(Not run)

Get Phenophases

Description

Retrieves a complete list of all phenophases in the NPN database.

Usage

npn_phenophases(...)

Arguments

Value

A tibble listing all phenophases available in the NPN database.

Examples

## Not run: 
phenophases <- npn_phenophases()

## End(Not run)

Get Phenophase for Species

Description

Retrieves the phenophases applicable to species for a given date. It's important to specify a date since protocols/phenophases for any given species can change from year to year.

Usage

npn_phenophases_by_species(species_ids, date, ...)

Arguments

Value

A tibble listing phenophases in the NPN database for the specified species and date.

Examples

## Not run: 
pp <- npn_phenophases_by_species(3, "2018-05-05")

## End(Not run)

Set Environment

Description

By default this library will call the NPN's production services but in some cases it's preferable to access the development web services so this function allows for manually setting the web service endpoints to use DEV instead. Just pass in "dev" to this function to change the endpoints to use.

Usage

npn_set_env(env = "ops")

Arguments

Get Species

Description

Returns a complete list of all species information of species represented in the NPN database.

Returns information about a species based on the NPN's unique ID for that species

Search for species by state

Search NPN species information using a number of different parameters, which can be used in conjunction with one another, including:

• Species on which a particular group or groups are actually collecting data

• What species were observed in a given date range

• What species were observed at a particular station or stations

Usage

npn_species(...)

npn_species_id(ids, ...)

npn_species_state(state, kingdom = NULL, ...)

npn_species_search(
  network = NULL,
  start_date = NULL,
  end_date = NULL,
  station_id = NULL,
  ...
)

Arguments

Value

A tibble with information on species in the NPN database and their IDs.

A tibble with information on species in the NPN database and their IDs, filtered by the species ID parameter.

A tibble with information on species in the NPN database whose distribution includes a given state.

A tibble with information on species in the NPN database filtered by partner group, dates and station/site IDs.

Examples

## Not run: 
npn_species()

## End(Not run)
## Not run: 
npn_species_id(ids = 3)

## End(Not run)
## Not run: 
npn_species_state(state = "AZ")
npn_species_state(state = "AZ", kingdom = "Plantae")

## End(Not run)
## Not run: 
species <- npn_species_search(
  start_date = "2013-01-01",
  end_date = "2013-05-15"
)

## End(Not run)

Get Species Types

Description

Return all plant or animal functional types used in the NPN database.

Usage

npn_species_types(kingdom = "Plantae", ...)

Arguments

Value

A data frame with a list of the functional types used in the NPN database, filtered by the specified kingdom.

Examples

## Not run: 
npn_species_types("Plantae")

## End(Not run)

Get Station Data

Description

Get a list of all stations, optionally filtered by state

Usage

npn_stations(state_code = NULL, ...)

Arguments

Value

A data frame with stations' latitude and longitude, names, and ids.

Examples

## Not run: 
npn_stations()
npn_stations('AZ')

## End(Not run)

Get station data based on a WKT defined geography.

Description

Takes a Well-Known Text based geography as input and returns data for all stations, including unique IDs, within that boundary.

Usage

npn_stations_by_location(wkt, ...)

Arguments

Value

A data frame listing stations filtered based on the WKT geography.

Examples

## Not run: 
head(npn_stations_by_state(wkt = "POLYGON((
-110.94484396954107 32.23623109416672,-110.96166678448247 32.23594069208043,
-110.95960684795904 32.21328646993733,-110.94244071026372 32.21343170728929,
-110.93935080547857 32.23216538049456,-110.94484396954107 32.23623109416672))")
)

## End(Not run)

Get number of stations by state.

Description

Get number of stations by state.

Usage

npn_stations_by_state(...)

Arguments

Value

A data frame listing stations by state.

Examples

## Not run: 
head(npn_stations_by_state())

## End(Not run)

Get Stations with Species

Description

Get a list of all stations which have an individual whom is a member of a set of species.

Usage

npn_stations_with_spp(species_id, ..., speciesid = deprecated())

Arguments

Value

A data frame with stations' latitude and longitude, names, and ids.

Examples

## Not run: 
npn_stations_with_spp(species_id = c(52, 53, 54))
npn_stations_with_spp(species_id = 53)

## End(Not run)

This function renamed to be consistent with other package function names.

Description

This function renamed to be consistent with other package function names.

Usage

npn_stationsbystate(...)

This function renamed to be consistent with other package function names.

Description

This function renamed to be consistent with other package function names.

Usage

npn_stationswithspp(...)

Resolve SIX Raster

Description

Utility function used to resolve the appropriate SI-x layer to use based on the year being retrieved, the phenophase and sub-model being requested.

Usage

resolve_six_raster(year, phenophase = "leaf", sub_model = NULL)

Arguments

Details

If the year being requested is more than two years older than the current year then use the prism based layers rather than the NCEP based layers. This is because the PRISM data is not available in whole until midway through the year after it was initially recorded. Hence, the 'safest' approach is to only refer to the PRISM data when we knows for sure it's available in full, i.e. two years prior.

Sub-model and phenophase on the other hand are appended to the name of the layer to request, no special logic is present in making the decision which layer to retrieve based on those parameters.

Value

Returns a terra::SpatRaster object of the appropriate SI-x layer.

Defunct functions in rnpn

Description

• npn_obsspbyday(): Removed.

• npn_allobssp(): Removed.

• npn_indspatstations(): Removed.

• npn_indsatstations(): Removed.

• npn_stationsbystate(): Removed.

• npn_stationswithspp(): Removed.