Load taxonomic reference lists, APC & APNI
Source:R/load_taxonomic_resources.R
load_taxonomic_resources.Rd
This function loads two taxonomic datasets for Australia's vascular plants, the APC and APNI, into the global environment. 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.
Examples
# \donttest{
load_taxonomic_resources(stable_or_current_data="stable",
version="0.0.2.9000")# }
#> Downloading...
#> File downloaded successfully.
#> File downloaded successfully.
#>
#> Loading resources into memory...
#>
===========================
=====================================================
================================================================================
#> ...done
#> $APC
#> # A tibble: 109,624 × 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 109,614 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: 132,385 × 48
#> scientific_name_ID name_type scientific_name scientificNameHTML
#> <chr> <chr> <chr> <chr>
#> 1 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… <scientific><name…
#> 2 https://id.biodiversity.org.au/… autonym Acanthus ebrac… <scientific><name…
#> 3 https://id.biodiversity.org.au/… scientif… Acanthus ebrac… <scientific><name…
#> 4 https://id.biodiversity.org.au/… autonym Acanthus ilici… <scientific><name…
#> 5 https://id.biodiversity.org.au/… scientif… Acanthus ilici… <scientific><name…
#> 6 https://id.biodiversity.org.au/… scientif… Acanthus ilici… <scientific><name…
#> 7 https://id.biodiversity.org.au/… scientif… Acanthus ilici… <scientific><name…
#> 8 https://id.biodiversity.org.au/… scientif… Acanthus molli… <scientific><name…
#> 9 https://id.biodiversity.org.au/… scientif… Acanthus volub… <scientific><name…
#> 10 https://id.biodiversity.org.au/… scientif… Acanthus L. <scientific><name…
#> # ℹ 132,375 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 list (accepted)`
#> # A tibble: 30,538 × 15
#> 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 30,528 more rows
#> # ℹ 10 more variables: accepted_name_usage_ID <chr>, name_type <chr>,
#> # taxon_rank <chr>, genus <chr>, stripped_canonical <chr>,
#> # stripped_canonical2 <chr>, stripped_scientific <chr>, binomial <chr>,
#> # trinomial <chr>, taxonomic_dataset <chr>
#>
#> $`APC list (known names)`
#> # A tibble: 69,647 × 15
#> canonical_name scientific_name taxonomic_status taxon_ID scientific_name_ID
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Pterostylis cli… Pterostylis cl… alternative name https:/… https://id.biodiv…
#> 2 Pterostylis cre… Pterostylis cr… alternative name https:/… https://id.biodiv…
#> 3 Eucalyptus resi… Eucalyptus res… alternative name https:/… https://id.biodiv…
#> 4 Macrozamia paul… Macrozamia pau… basionym https:/… https://id.biodiv…
#> 5 Lycopodium creb… Lycopodium cre… basionym https:/… https://id.biodiv…
#> 6 Lycopodium lock… Lycopodium loc… basionym https:/… https://id.biodiv…
#> 7 Aralia polaris Aralia polaris… basionym https:/… https://id.biodiv…
#> 8 Sium nodiflorum Sium nodifloru… basionym https:/… https://id.biodiv…
#> 9 Trachymene koch… Trachymene koc… basionym https:/… https://id.biodiv…
#> 10 Pittosporum res… Pittosporum re… basionym https:/… https://id.biodiv…
#> # ℹ 69,637 more rows
#> # ℹ 10 more variables: accepted_name_usage_ID <chr>, name_type <chr>,
#> # taxon_rank <chr>, genus <chr>, stripped_canonical <chr>,
#> # stripped_canonical2 <chr>, stripped_scientific <chr>, binomial <chr>,
#> # trinomial <chr>, taxonomic_dataset <chr>
#>
#> $`APNI names`
#> # A tibble: 15,379 × 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 15,369 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: 3,094 × 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 3,084 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: 2,848 × 11
#> canonical_name accepted_name_usage accepted_name_usage_ID scientific_name
#> <chr> <chr> <chr> <chr>
#> 1 Encephallartes Encephalartos Lehm. https://id.biodiversity… Encephallartes…
#> 2 Encephalartus Encephalartos Lehm. https://id.biodiversity… Encephalartus …
#> 3 Encephalartos Encephalartos Lehm. https://id.biodiversity… Encephalartos …
#> 4 Catakidozamia Lepidozamia Regel https://id.biodiversity… Catakidozamia …
#> 5 Zamia Zamia L. https://id.biodiversity… Zamia L.
#> 6 Calamaria Isoetes L. https://id.biodiversity… Calamaria Boeh…
#> 7 Lateristachys Lycopodiella Holub https://id.biodiversity… Lateristachys …
#> 8 Lepidotis Lycopodiella Holub https://id.biodiversity… Lepidotis P.Be…
#> 9 Austrolycopodium Lycopodium L. https://id.biodiversity… Austrolycopodi…
#> 10 Diphasium Lycopodium L. https://id.biodiversity… Diphasium C.Pr…
#> # ℹ 2,838 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: 1,426 × 8
#> canonical_name scientific_name taxonomic_status scientific_name_ID name_type
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Beloperone Beloperone Nees unplaced https://id.biodiv… scientif…
#> 2 Hemiadelphis Hemiadelphis Ne… unplaced https://id.biodiv… scientif…
#> 3 Leptosiphonium Leptosiphonium … unplaced https://id.biodiv… scientif…
#> 4 Megaskepasma Megaskepasma Li… unplaced https://id.biodiv… scientif…
#> 5 Meyenia Meyenia Nees unplaced https://id.biodiv… scientif…
#> 6 Simonachne Simonachne E.J.… unplaced https://id.biodiv… scientif…
#> 7 Thyrsacanthus Thyrsacanthus N… unplaced https://id.biodiv… scientif…
#> 8 Synarrhena Synarrhena F.Mu… unplaced https://id.biodiv… scientif…
#> 9 Allosorus Allosorus Bernh. unplaced https://id.biodiv… scientif…
#> 10 Austrogramme Austrogramme E.… unplaced https://id.biodiv… scientif…
#> # ℹ 1,416 more rows
#> # ℹ 3 more variables: taxon_rank <chr>, genus <chr>, taxonomic_dataset <chr>
#>
#> $genera_all
#> # A tibble: 7,368 × 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 7,358 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 Compositae Asteraceae Bercht. … https://id.biodiversi… Compositae Gis…
#> # 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>
#>