spfungorum_records

Retrieve Species Fungorum (Index Fungorum) records for a taxon, filtered to Brazil evidence

fungaR::spfungorum_records()

Description

Given a fungal species or genus, retrieves every matching name from Species Fungorum (the nomenclatural database maintained by the Royal Botanic Gardens, Kew, also known as Index Fungorum) and, by default, filters the result down to only the names whose own reported locality places them in Brazil - returning a structured spreadsheet of Index Fungorum information (including each name’s original Species Fungorum URL) for those Brazilian records. Like mycobank_records, this is a straightforward retrieval tool, not a gap/comparison one - it does not cross-check FFB at all.

Details

Species Fungorum/Index Fungorum has no bulk export, but it does publish a public, documented web service (https://www.indexfungorum.org/ixfwebservice/fungus.asmx) that answers plain HTTP GET requests with XML - no SOAP client, headless browser, or authentication required. A single request returns every name matching taxon, including, for many records, the type specimen’s own reported LOCATION and HOST fields - the data this function uses as its Brazil-evidence signal. Unlike MycoBank, no per-record page visit is needed: everything comes back in one response.

Index Fungorum’s LOCATION field very often names a Brazilian state directly (e.g. "Pernambuco") rather than the country itself, so Fungorum_Brazil_Evidence checks Fungorum_Location against the country name and every Brazilian state name (with or without diacritics), not just the literal word “Brazil”.

Arguments

Argument	Description
taxon	Character. A single fungal species or genus name (e.g. `"Phellinotus neoaridus"` or `"Phellinotus"`).
rank	Character. Whether `taxon` is a `"species"` (default) or a `"genus"`. Species Fungorum’s web service has no operation for searching by higher classification (order/family), so `rank = "order"` is not supported.
require_brazil_evidence	Logical. If `TRUE` (default), the returned table is filtered to only the names whose Index Fungorum `Location` mentions Brazil (the country name or any Brazilian state). Set to `FALSE` to instead return every matching name regardless of locality, for manual review.
fetch_details	Logical. If `TRUE` (default), each returned name’s own Species Fungorum page is visited (a fast, plain HTTP request - no headless browser, unlike MycoBank) to read the journal it was published in, the full formatted citation, the basionym or typification details, the current name’s own full citation, and the Index Fungorum LSID - none of which are in the bulk `NameSearch` response. Set to `FALSE` to skip this and return only the fields already in that response.
max_number	Numeric. Maximum number of matching names requested from the web service in a single call. Defaults to `1000`, generous for any genus.
verbose	Logical. If `TRUE` (default), prints progress messages.
save	Logical. If `TRUE` (default), the result is saved to disk as an `.xlsx` spreadsheet.
dir	Character. Directory where the spreadsheet is saved when `save = TRUE`. Defaults to `"spfungorum_records"`.
filename	Character. Name of the `.xlsx` file (without extension) to save. Defaults to `"spfungorum_records_<taxon>"`.
html_report	Logical. If `TRUE` (default), also writes a self-contained HTML report (`<dir>/<filename>.html`) summarizing the results: KPI counts and the full record table as a sortable, filterable DT widget with buttons to copy or download it as CSV/Excel. Requires the rmarkdown, DT, and htmltools packages; if any is missing, the report is skipped with a message (the `.xlsx` spreadsheet is unaffected).
open_report	Logical. If `TRUE` (default in interactive sessions), opens the rendered HTML report in the default browser.

Value

A data.frame, one row per matching Index Fungorum name and, by default, with a Brazilian reported locality, with columns:

Fungorum_NumberIndex Fungorum’s numeric record identifier for the name. Taxon_nameThe binomial as registered in Index Fungorum. AuthorsAuthor citation. SpecificEpithetThe bare specific epithet. YearYear of publication. Name_statusIndex Fungorum’s nomenclatural status (e.g. "Legitimate"). Current_nameIndex Fungorum’s currently accepted name for this entry, when different (i.e. when Taxon_name is itself a synonym). When fetch_details = TRUE, this is the freshly-scraped value from the name’s own page rather than the bulk search response’s own (occasionally stale) field. Fungorum_Location, Fungorum_HostType specimen locality and host, as reported in Index Fungorum’s own record (may be NA - not every record has these). Volume, Part, PageThe publication’s volume, part/issue, and page. PublishingAuthorsFull author list of the publication the name appeared in, which may differ from Authors (the name’s own author citation). Fungorum_URLDirect link to the name’s Species Fungorum page. Fungorum_JournalThe journal the name was published in (only when fetch_details = TRUE; not available from the bulk search response). Fungorum_CitationThe full formatted citation as shown on the name’s own Species Fungorum page (only when fetch_details = TRUE). Fungorum_BasionymThe basionym or typification details, when present (only when fetch_details = TRUE). Fungorum_Current_Name_CitationThe full citation of the currently accepted name (only when fetch_details = TRUE). Fungorum_LSIDThe Index Fungorum Life Science Identifier (only when fetch_details = TRUE). Fungorum_Brazil_EvidenceLogical; TRUE when Fungorum_Location mentions Brazil (the country or any Brazilian state).

Examples

# All Index Fungorum information for a single species, only if it reports a
# Brazilian locality
sp <- spfungorum_records(taxon = "Phellinotus neoaridus")

# Every Index Fungorum species-level name in genus Phellinotus with a
# Brazilian reported locality
genus_records <- spfungorum_records(taxon = "Phellinotus", rank = "genus")

# Every matching name regardless of locality, for manual review
all_records <- spfungorum_records(taxon = "Phellinotus", rank = "genus",
                                      require_brazil_evidence = FALSE)

--- title: 'spfungorum_records' description: 'Retrieve Species Fungorum (Index Fungorum) records for a taxon, filtered to Brazil evidence' toc: true toc-depth: 3 --- ```{r} #| eval: false fungaR::spfungorum_records() ``` ### Description Given a fungal species or genus, retrieves every matching name from [Species Fungorum](https://www.speciesfungorum.org) (the nomenclatural database maintained by the Royal Botanic Gardens, Kew, also known as Index Fungorum) and, by default, filters the result down to only the names whose own reported locality places them in Brazil - returning a structured spreadsheet of Index Fungorum information (including each name's original Species Fungorum URL) for those Brazilian records. Like `mycobank_records`, this is a straightforward retrieval tool, not a gap/comparison one - it does not cross-check FFB at all. ### Details Species Fungorum/Index Fungorum has no bulk export, but it does publish a public, documented web service (https://www.indexfungorum.org/ixfwebservice/fungus.asmx) that answers plain HTTP GET requests with XML - no SOAP client, headless browser, or authentication required. A single request returns every name matching `taxon`, including, for many records, the type specimen's own reported `LOCATION` and `HOST` fields - the data this function uses as its Brazil-evidence signal. Unlike MycoBank, no per-record page visit is needed: everything comes back in one response. Index Fungorum's `LOCATION` field very often names a Brazilian state directly (e.g. `"Pernambuco"`) rather than the country itself, so `Fungorum_Brazil_Evidence` checks `Fungorum_Location` against the country name and every Brazilian state name (with or without diacritics), not just the literal word "Brazil". ### Arguments | Argument | Description | |---|---| | taxon | Character. A single fungal species or genus name (e.g. `"Phellinotus neoaridus"` or `"Phellinotus"`). | | rank | Character. Whether `taxon` is a `"species"` (default) or a `"genus"`. Species Fungorum's web service has no operation for searching by higher classification (order/family), so `rank = "order"` is not supported. | | require_brazil_evidence | Logical. If `TRUE` (default), the returned table is filtered to only the names whose Index Fungorum `Location` mentions Brazil (the country name or any Brazilian state). Set to `FALSE` to instead return every matching name regardless of locality, for manual review. | | fetch_details | Logical. If `TRUE` (default), each returned name's own Species Fungorum page is visited (a fast, plain HTTP request - no headless browser, unlike MycoBank) to read the journal it was published in, the full formatted citation, the basionym or typification details, the current name's own full citation, and the Index Fungorum LSID - none of which are in the bulk `NameSearch` response. Set to `FALSE` to skip this and return only the fields already in that response. | | max_number | Numeric. Maximum number of matching names requested from the web service in a single call. Defaults to `1000`, generous for any genus. | | verbose | Logical. If `TRUE` (default), prints progress messages. | | save | Logical. If `TRUE` (default), the result is saved to disk as an `.xlsx` spreadsheet. | | dir | Character. Directory where the spreadsheet is saved when `save = TRUE`. Defaults to `"spfungorum_records"`. | | filename | Character. Name of the `.xlsx` file (without extension) to save. Defaults to `"spfungorum_records_<taxon>"`. | | html_report | Logical. If `TRUE` (default), also writes a self-contained HTML report (`<dir>/<filename>.html`) summarizing the results: KPI counts and the full record table as a sortable, filterable DT widget with buttons to copy or download it as CSV/Excel. Requires the rmarkdown, DT, and htmltools packages; if any is missing, the report is skipped with a message (the `.xlsx` spreadsheet is unaffected). | | open_report | Logical. If `TRUE` (default in interactive sessions), opens the rendered HTML report in the default browser. | ### Value A `data.frame`, one row per matching Index Fungorum name and, by default, with a Brazilian reported locality, with columns: Fungorum_NumberIndex Fungorum's numeric record identifier for the name. Taxon_nameThe binomial as registered in Index Fungorum. AuthorsAuthor citation. SpecificEpithetThe bare specific epithet. YearYear of publication. Name_statusIndex Fungorum's nomenclatural status (e.g. `"Legitimate"`). Current_nameIndex Fungorum's currently accepted name for this entry, when different (i.e. when `Taxon_name` is itself a synonym). When `fetch_details = TRUE`, this is the freshly-scraped value from the name's own page rather than the bulk search response's own (occasionally stale) field. Fungorum_Location, Fungorum_HostType specimen locality and host, as reported in Index Fungorum's own record (may be `NA` - not every record has these). Volume, Part, PageThe publication's volume, part/issue, and page. PublishingAuthorsFull author list of the publication the name appeared in, which may differ from `Authors` (the name's own author citation). Fungorum_URLDirect link to the name's Species Fungorum page. Fungorum_JournalThe journal the name was published in (only when `fetch_details = TRUE`; not available from the bulk search response). Fungorum_CitationThe full formatted citation as shown on the name's own Species Fungorum page (only when `fetch_details = TRUE`). Fungorum_BasionymThe basionym or typification details, when present (only when `fetch_details = TRUE`). Fungorum_Current_Name_CitationThe full citation of the currently accepted name (only when `fetch_details = TRUE`). Fungorum_LSIDThe Index Fungorum Life Science Identifier (only when `fetch_details = TRUE`). Fungorum_Brazil_EvidenceLogical; `TRUE` when `Fungorum_Location` mentions Brazil (the country or any Brazilian state). ### Examples ```r # All Index Fungorum information for a single species, only if it reports a # Brazilian locality sp <- spfungorum_records(taxon = "Phellinotus neoaridus") # Every Index Fungorum species-level name in genus Phellinotus with a # Brazilian reported locality genus_records <- spfungorum_records(taxon = "Phellinotus", rank = "genus") # Every matching name regardless of locality, for manual review all_records <- spfungorum_records(taxon = "Phellinotus", rank = "genus", require_brazil_evidence = FALSE) ```