Check the native status for plant species in a political region

Description

NSR returns information on native status for species within a political region.

Usage

NSR(occurrence_dataframe, ...)

Arguments

Value

Dataframe containing NSR results.

Examples

## Not run: 

results <- NSR(occurrence_dataframe = nsr_testfile)
  
# Inspect the results
head(results, 10)
# That's a lot of columns. Let's display one row vertically
# to get a better understanding of the output fields
results.t <- t(results[,2:ncol(results)]) 
results.t[,1,drop =FALSE]
# Summarize the main results
results[ 1:10, 
c("species", "country", "state_province", "native_status", "native_status_reason")]

# Compare summary flag isIntroduced to more detailed native_status values
# and inspect souces consulted
results[ 1:10, 
c("species", "country", "state_province", "native_status", "isIntroduced", "native_status_sources")]





## End(Not run)

Get citation information

Description

Returns information needed to cite the NSR

Usage

NSR_citations(...)

Arguments

Value

Dataframe containing bibtex-formatted citation information

Note

This function provides citation information in bibtex format that can be used with reference manager software (e.g. Paperpile, Zotero). Please do remember to cite both the sources and the NSR, as the NSR couldn't exist without these sources!

Examples

{
citation_info <- NSR_citations()
}

Get NSR data dictionary

Description

Returns information from the NSR data dictionary

Usage

NSR_data_dictionary(native_status = FALSE, ...)

Arguments

Value

Data.frame containing requested data dictionary contents.

Examples

{
NSR_fields <- NSR_data_dictionary()

status_codes <- NSR_data_dictionary(native_status = TRUE)
}

Get NSR metadata

Description

Returns metadata on NSR including version and citation information

Usage

NSR_metadata(bibtex_file = NULL, ...)

Arguments

Value

List containing: (1) bibtex-formatted citation information, (2) information about NSR data sources, and (3) NSR version information.

Note

This function provides citation information in bibtex format that can be used with reference manager software (e.g. Paperpile, Zotero). Please remember to cite both the sources and the NSR, as the NSR couldn't exist without these sources!

This function is a wrapper that returns the output of the functions NSR_citations, NSR_sources, and NSR_version.

Examples

{
metadata <- NSR_metadata()
}

Get information on political divisions with checklists within the NSR

Description

NSR_political_divisions returns information on political divisions with checklist information present in the NSR.

Usage

NSR_political_divisions(by_country = TRUE, ...)

Arguments

Value

data.frame containing information on political divisions within the NSR database.

Note

Setting checklist to FALSE returns a list of political divisions that can be used to standardize spellings.

Examples

## Not run: 

#To get a list of all political divisions with comprehensive checklists:
checklists_per_country <- NSR_political_divisions()

#To get a list of all checklists the associated countries, set "by_country" to FALSE
countries_per_checklist <- NSR_political_divisions(by_country=FALSE)


## End(Not run)

Check the native status for plant species in a political region

Description

NSR_simple returns information on native status for species within a political region.

Usage

NSR_simple(
  species = NULL,
  country = NULL,
  state_province = NULL,
  county_parish = NULL,
  ...
)

Arguments

Value

Dataframe containing NSR results.

Examples

## Not run: 

results <- NSR_simple(species = "Acer rubrum",
           country = "Canada",state_province = "Ontario")

results <- NSR_simple(species = c("Acer rubrum", "Aspen tremuloides") , 
           country = c("Canada","Canada"),state_province = c("Ontario","Ontario"))


## End(Not run)

Get information on sources used by the NSR

Description

Return metadata about the current NSR sources

Usage

NSR_sources(...)

Arguments

Value

Dataframe containing information about the sources used in the current NSR version.

Examples

{
sources <- NSR_sources()
}

Make a template for an NSR query

Description

NSR_template builds a template that can be populated to submit an NSR query.

Usage

NSR_template(nrow = 1)

Arguments

Value

Template data.frame that can be populated and then used in NSR queries.

Examples

## Not run: 

template<-NSR_template(nrow = 2)
template$genus<-"Acer"
template$species<-c("Acer rubrum", "Acer saccharum")
template$country<-"Canada"
template$user_id<-1:2
results <- NSR(occurrence_dataframe = template)


## End(Not run)

Get metadata on current NSR version

Description

Return metadata about the current NSR version

Usage

NSR_version(...)

Arguments

Value

Dataframe containing current NSR version number, build date, and code version.

Examples

{
NSR_version_metadata <- NSR_version()
}

Check whether the internet is on

Description

Check for internet

Usage

check_internet()

Value

TRUE if internet connection is detected, FALSE otherwise.

Handle API access and format

Description

Internal function for handling accessing the API,data formatting, and errors

Usage

nsr_core(
  url = "https://nsrapi.xyz/nsr_wsb.php",
  mode,
  data_json = NULL,
  batches = NULL,
  skip_internet_check = FALSE
)

Arguments

Example NSR data

Description

A sample dataset showing the proper formatting of NSR inputs.

Usage

nsr_testfile

Format

A data.frame with 22 observations of 5 variables:

taxon

taxon, "Genus species" format, with specific epithet optional

country

country that a species occurs within

state_province

state/province that a species occurs within

county_parish

county/parish that a species occurs within

user_id

unique numeric ID that can be used to link to original dataset

...

Source

https://biendata.org