Load taxonomic reference lists, APC & APNI
Source:R/load_taxonomic_resources.R
load_taxonomic_resources.RdThis function loads two taxonomic datasets for Australia's vascular plants, the APC and APNI. It creates several data frames by filtering and selecting data from the loaded lists.
Usage
load_taxonomic_resources(
stable_or_current_data = "stable",
version = default_version(),
quiet = FALSE
)Arguments
- stable_or_current_data
Type of dataset to access. The default is "stable", which loads the dataset from a github archived file. If set to "current", the dataset will be loaded from a URL which is the cutting edge version, but this may change at any time without notice.
- version
The version number of the dataset to use. Defaults to the default version.
- quiet
A logical indicating whether to print status of loading to screen. Defaults to FALSE.
Details
It accesses taxonomic data from a dataset using the provided version number or the default version.
The output is several dataframes that include subsets of the APC/APNI based on taxon rank and taxonomic status.
Results are cached in memory for the R session so that repeated calls with the same
versionandstable_or_current_dataarguments return immediately without re-downloading or re-processing the data. Useclear_cached_resources()to force a reload."current"data is not cached because it may change between calls.
Examples
# \donttest{
load_taxonomic_resources(stable_or_current_data="stable",
version="2024-10-11")# }
#> Downloading...
#> File downloaded successfully.
#> File downloaded successfully.
#>
#> Loading resources into memory...
#>
===========================
=====================================================
================================================================================
#> ...done
#> $APC
#> # A tibble: 109,883 × 38
#> taxon_ID name_type accepted_name_usage_ID accepted_name_usage
#> <chr> <chr> <chr> <chr>
#> 1 https://id.biodiversity… scientif… https://id.biodiversi… Plantae Haeckel
#> 2 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs
#> 3 https://id.biodiversity… scientif… https://id.biodiversi… Charophyta Sachs
#> 4 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag…
#> 5 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag…
#> 6 https://id.biodiversity… scientif… https://id.biodiversi… Equisetopsida C.Ag…
#> 7 https://id.biodiversity… scientif… https://id.biodiversi… Cycadidae Pax
#> 8 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex…
#> 9 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex…
#> 10 https://id.biodiversity… scientif… https://id.biodiversi… Cycadales Pers. ex…
#> # ℹ 109,873 more rows
#> # ℹ 34 more variables: nomenclaturalStatus <chr>, nomIlleg <chr>,
#> # nomInval <chr>, taxonomic_status <chr>, pro_parte <lgl>,
#> # scientific_name <chr>, scientific_name_ID <chr>, canonical_name <chr>,
#> # scientific_name_authorship <chr>, parentNameUsageID <chr>,
#> # taxon_rank <chr>, taxon_rank_sort_order <dbl>, kingdom <chr>, class <chr>,
#> # subclass <chr>, family <chr>, taxonConceptID <chr>, …
#>
#> $APNI
#> # A tibble: 24,562 × 48
#> scientific_name_ID name_type scientific_name scientificNameHTML
#> <chr> <chr> <chr> <chr>
#> 1 https://id.biodiversity.org.au/… autonym Acanthus ebrac… <scientific><name…
#> 2 https://id.biodiversity.org.au/… autonym Acanthus ilici… <scientific><name…
#> 3 https://id.biodiversity.org.au/… scientif… Acanthus ilici… <scientific><name…
#> 4 https://id.biodiversity.org.au/… scientif… Acanthus ilici… <scientific><name…
#> 5 https://id.biodiversity.org.au/… scientif… Acanthus volub… <scientific><name…
#> 6 https://id.biodiversity.org.au/… scientif… Asystasia chel… <scientific><name…
#> 7 https://id.biodiversity.org.au/… phrase-n… Asystasia sp. … <scientific><name…
#> 8 https://id.biodiversity.org.au/… scientif… Avicennia alba… <scientific><name…
#> 9 https://id.biodiversity.org.au/… scientif… Avicennia alba… <scientific><name…
#> 10 https://id.biodiversity.org.au/… scientif… Avicennia mind… <scientific><name…
#> # ℹ 24,552 more rows
#> # ℹ 44 more variables: canonical_name <chr>, canonicalNameHTML <chr>,
#> # name_element <chr>, nomenclaturalStatus <chr>,
#> # scientific_name_authorship <chr>, autonym <lgl>, hybrid <lgl>,
#> # cultivar <lgl>, formula <lgl>, scientific <lgl>, nomInval <lgl>,
#> # nomIlleg <lgl>, namePublishedIn <chr>, namePublishedInID <chr>,
#> # namePublishedInYear <dbl>, nameInstanceType <chr>, …
#>
#> $APC_accepted
#> # A tibble: 30,565 × 16
#> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Cycas angulata Cycas angulata… accepted https:/… https://id.biodiv…
#> 2 Cycas arenicola Cycas arenicol… accepted https:/… https://id.biodiv…
#> 3 Cycas armstrong… Cycas armstron… accepted https:/… https://id.biodiv…
#> 4 Cycas arnhemica Cycas arnhemic… accepted https:/… https://id.biodiv…
#> 5 Cycas badensis Cycas badensis… accepted https:/… https://id.biodiv…
#> 6 Cycas basaltica Cycas basaltic… accepted https:/… https://id.biodiv…
#> 7 Cycas brunnea Cycas brunnea … accepted https:/… https://id.biodiv…
#> 8 Cycas cairnsiana Cycas cairnsia… accepted https:/… https://id.biodiv…
#> 9 Cycas calcicola Cycas calcicol… accepted https:/… https://id.biodiv…
#> 10 Cycas canalis Cycas canalis … accepted https:/… https://id.biodiv…
#> # ℹ 30,555 more rows
#> # ℹ 11 more variables: accepted_name_usage_ID <chr>, name_type <chr>,
#> # taxon_rank <chr>, family <chr>, genus <chr>, stripped_canonical <chr>,
#> # stripped_canonical2 <chr>, stripped_scientific <chr>, binomial <chr>,
#> # trinomial <chr>, taxonomic_dataset <chr>
#>
#> $APC_synonyms
#> # A tibble: 69,850 × 16
#> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Cycas arnhemica… Cycas arnhemic… taxonomic synon… https:/… https://id.biodiv…
#> 2 Cycas arnhemica… Cycas arnhemic… taxonomic synon… https:/… https://id.biodiv…
#> 3 Cycas canalis s… Cycas canalis … taxonomic synon… https:/… https://id.biodiv…
#> 4 Cycas sp., Pine… Cycas sp., Pin… taxonomic synon… https:/… https://id.biodiv…
#> 5 Cycas sp. 'Pine… Cycas sp. 'Pin… taxonomic synon… https:/… https://id.biodiv…
#> 6 Cycas maconochi… Cycas maconoch… taxonomic synon… https:/… https://id.biodiv…
#> 7 Cycas kennedyana Cycas kennedya… taxonomic synon… https:/… https://id.biodiv…
#> 8 Cycas gracilis … Cycas gracilis… taxonomic synon… https:/… https://id.biodiv…
#> 9 Cycas gracilis … Cycas gracilis… taxonomic synon… https:/… https://id.biodiv…
#> 10 Cycas rumphii s… Cycas rumphii … taxonomic synon… https:/… https://id.biodiv…
#> # ℹ 69,840 more rows
#> # ℹ 11 more variables: accepted_name_usage_ID <chr>, name_type <chr>,
#> # taxon_rank <chr>, family <chr>, genus <chr>, stripped_canonical <chr>,
#> # stripped_canonical2 <chr>, stripped_scientific <chr>, binomial <chr>,
#> # trinomial <chr>, taxonomic_dataset <chr>
#>
#> $APNI_names
#> # A tibble: 12,204 × 13
#> canonical_name scientific_name scientific_name_ID name_type taxon_rank
#> <chr> <chr> <chr> <chr> <chr>
#> 1 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species
#> 2 (Eucalyptus globulus… (Eucalyptus gl… https://id.biodiv… hybrid-f… species
#> 3 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species
#> 4 (Eucalyptus johnston… (Eucalyptus jo… https://id.biodiv… hybrid-f… species
#> 5 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species
#> 6 (Eucalyptus urnigera… (Eucalyptus ur… https://id.biodiv… hybrid-f… species
#> 7 Abacopteris presliana Abacopteris pr… https://id.biodiv… scientif… species
#> 8 Abarema clypearia f.… Abarema clypea… https://id.biodiv… scientif… form
#> 9 Abarema pruinosa Abarema pruino… https://id.biodiv… scientif… species
#> 10 Abelia rupestris Abelia rupestr… https://id.biodiv… scientif… species
#> # ℹ 12,194 more rows
#> # ℹ 8 more variables: taxonomic_status <chr>, stripped_canonical <chr>,
#> # stripped_canonical2 <chr>, stripped_scientific <chr>, binomial <chr>,
#> # trinomial <chr>, genus <chr>, taxonomic_dataset <chr>
#>
#> $genera_accepted
#> # A tibble: 3,093 × 11
#> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name
#> <chr> <chr> <chr> <chr>
#> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L.
#> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f.
#> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re…
#> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq.
#> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L.
#> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L.
#> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh.
#> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H…
#> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L.
#> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus …
#> # ℹ 3,083 more rows
#> # ℹ 7 more variables: taxonomic_status <chr>, taxon_ID <chr>,
#> # scientific_name_ID <chr>, name_type <chr>, taxon_rank <chr>, genus <chr>,
#> # taxonomic_dataset <chr>
#>
#> $genera_synonym
#> # A tibble: 2,858 × 11
#> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name
#> <chr> <chr> <chr> <chr>
#> 1 Catakidozamia Lepidozamia Regel https://id.biodiversit… Catakidozamia …
#> 2 Calamaria Isoetes L. https://id.biodiversit… Calamaria Boeh…
#> 3 Lepidotis Lycopodiella Holub https://id.biodiversit… Lepidotis P.Be…
#> 4 Lateristachys Lycopodiella Holub https://id.biodiversit… Lateristachys …
#> 5 Pseudodiphasium Lycopodium L. https://id.biodiversit… Pseudodiphasiu…
#> 6 Diphasium Lycopodium L. https://id.biodiversit… Diphasium C.Pr…
#> 7 Austrolycopodium Lycopodium L. https://id.biodiversit… Austrolycopodi…
#> 8 Pseudolycopodium Lycopodium L. https://id.biodiversit… Pseudolycopodi…
#> 9 Stachygynandrum Selaginella P.Beauv. https://id.biodiversit… Stachygynandru…
#> 10 Lycopodioides Selaginella P.Beauv. https://id.biodiversit… Lycopodioides …
#> # ℹ 2,848 more rows
#> # ℹ 7 more variables: taxonomic_status <chr>, taxon_ID <chr>,
#> # scientific_name_ID <chr>, name_type <chr>, taxon_rank <chr>, genus <chr>,
#> # taxonomic_dataset <chr>
#>
#> $genera_APNI
#> # A tibble: 1,228 × 8
#> canonical_name scientific_name taxonomic_status scientific_name_ID name_type
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Hemiadelphis Hemiadelphis Ne… unplaced https://id.biodiv… scientif…
#> 2 Leptosiphonium Leptosiphonium … unplaced https://id.biodiv… scientif…
#> 3 Meyenia Meyenia Nees unplaced https://id.biodiv… scientif…
#> 4 Simonachne Simonachne E.J.… unplaced https://id.biodiv… scientif…
#> 5 Thyrsacanthus Thyrsacanthus N… unplaced https://id.biodiv… scientif…
#> 6 Synarrhena Synarrhena F.Mu… unplaced https://id.biodiv… scientif…
#> 7 Allosorus Allosorus Bernh. unplaced https://id.biodiv… scientif…
#> 8 Austrogramme Austrogramme E.… unplaced https://id.biodiv… scientif…
#> 9 Neurogramme Neurogramme Die… unplaced https://id.biodiv… scientif…
#> 10 Chlamydia Chlamydia Gaert… unplaced https://id.biodiv… scientif…
#> # ℹ 1,218 more rows
#> # ℹ 3 more variables: taxon_rank <chr>, genus <chr>, taxonomic_dataset <chr>
#>
#> $genera_all
#> # A tibble: 7,179 × 12
#> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name
#> <chr> <chr> <chr> <chr>
#> 1 Cycas Cycas L. https://id.biodiversity.o… Cycas L.
#> 2 Bowenia Bowenia Hook.f. https://id.biodiversity.o… Bowenia Hook.f.
#> 3 Lepidozamia Lepidozamia Regel https://id.biodiversity.o… Lepidozamia Re…
#> 4 Macrozamia Macrozamia Miq. https://id.biodiversity.o… Macrozamia Miq.
#> 5 Equisetum Equisetum L. https://id.biodiversity.o… Equisetum L.
#> 6 Isoetes Isoetes L. https://id.biodiversity.o… Isoetes L.
#> 7 Huperzia Huperzia Bernh. https://id.biodiversity.o… Huperzia Bernh.
#> 8 Lycopodiella Lycopodiella Holub https://id.biodiversity.o… Lycopodiella H…
#> 9 Lycopodium Lycopodium L. https://id.biodiversity.o… Lycopodium L.
#> 10 Phlegmariurus Phlegmariurus Holub https://id.biodiversity.o… Phlegmariurus …
#> # ℹ 7,169 more rows
#> # ℹ 8 more variables: taxonomic_status <chr>, taxon_ID <chr>,
#> # scientific_name_ID <chr>, name_type <chr>, taxon_rank <chr>, genus <chr>,
#> # taxonomic_dataset <chr>, cleaned_name <chr>
#>
#> $family_accepted
#> # A tibble: 307 × 38
#> taxon_ID name_type accepted_name_usage_ID accepted_name_usage
#> <chr> <chr> <chr> <chr>
#> 1 https://id.biodiversity… scientif… https://id.biodiversi… Cycadaceae Pers.
#> 2 https://id.biodiversity… scientif… https://id.biodiversi… Zamiaceae Horan.
#> 3 https://id.biodiversity… scientif… https://id.biodiversi… Equisetaceae Michx…
#> 4 https://id.biodiversity… scientif… https://id.biodiversi… Isoetaceae Rchb.
#> 5 https://id.biodiversity… scientif… https://id.biodiversi… Lycopodiaceae P.Be…
#> 6 https://id.biodiversity… scientif… https://id.biodiversi… Selaginellaceae Wi…
#> 7 https://id.biodiversity… scientif… https://id.biodiversi… Apiaceae Lindl.
#> 8 https://id.biodiversity… scientif… https://id.biodiversi… Araliaceae Juss.
#> 9 https://id.biodiversity… scientif… https://id.biodiversi… Griseliniaceae J.R…
#> 10 https://id.biodiversity… scientif… https://id.biodiversi… Myodocarpaceae Dow…
#> # ℹ 297 more rows
#> # ℹ 34 more variables: nomenclaturalStatus <chr>, nomIlleg <chr>,
#> # nomInval <chr>, taxonomic_status <chr>, pro_parte <lgl>,
#> # scientific_name <chr>, scientific_name_ID <chr>, canonical_name <chr>,
#> # scientific_name_authorship <chr>, parentNameUsageID <chr>,
#> # taxon_rank <chr>, taxon_rank_sort_order <dbl>, kingdom <chr>, class <chr>,
#> # subclass <chr>, family <chr>, taxonConceptID <chr>, …
#>
#> $family_synonym
#> # A tibble: 244 × 11
#> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name
#> <chr> <chr> <chr> <chr>
#> 1 Boweniaceae Zamiaceae Horan. https://id.biodiversi… Boweniaceae D.…
#> 2 Lycopodia Lycopodiaceae P.Bea… https://id.biodiversi… Lycopodia Mirb.
#> 3 Umbelliferae Apiaceae Lindl. https://id.biodiversi… Umbelliferae J…
#> 4 Araliae Araliaceae Juss. https://id.biodiversi… Araliae Juss.
#> 5 Griselineae Griseliniaceae J.R.… https://id.biodiversi… Griselineae A.…
#> 6 Pittosporeae Pittosporaceae R.Br. https://id.biodiversi… Pittosporeae R…
#> 7 Cardiopterideae Cardiopteridaceae B… https://id.biodiversi… Cardiopteridea…
#> 8 Quintiniaceae Paracryphiaceae Air… https://id.biodiversi… Quintiniaceae …
#> 9 Sphenostemonaceae Paracryphiaceae Air… https://id.biodiversi… Sphenostemonac…
#> 10 Astereae Asteraceae Bercht. … https://id.biodiversi… Astereae Berch…
#> # ℹ 234 more rows
#> # ℹ 7 more variables: taxonomic_status <chr>, taxon_ID <chr>,
#> # scientific_name_ID <chr>, name_type <chr>, taxon_rank <chr>, genus <chr>,
#> # taxonomic_dataset <chr>
#>