Only queries galah for taxa not already in taxonomy_file. Can return a list,
for several levels of taxonomic hierarchy, with the 'best' match at that
level. For example, if 'genus' is provided in needed_ranks, the returned
list will have an element 'genus' that contains, in a column named taxa,
and for each of the original names provided, the best result at genus level
or higher (in cases where no genus level match was available).
make_taxonomy(
df = NULL,
taxa_col = "original_name",
taxonomy_file = tempfile(),
force_new = list(original_name = NULL, timediff = as.difftime(26, units = "weeks")),
remove_taxa = c("bold:", "unverified", "undetermined", "unidentified", "annual herb",
"annual grass", "incertae sedis", "\\?", "another\\s", "not naturalised in sa",
"annual tussock grass", "*no id", "spec\\.", "aquatic grass"),
remove_strings = c("\\s\\-\\-\\s.*", "\\ssp\\.$", "\\sssp\\.$",
"\\sspec\\.$", "\\ssp$", "\\sssp$", "\\ssp\\d$", "dead", "\\sx\\s.*",
"\\sX\\s.*", "unknown", "\\scultivar$", "\\scomplex$", "\\(NC\\)",
"\\saff\\."),
not_names = c("sp", "ssp", "var", "subsp", "subspecies", "form", "race", "nov", "aff",
"cf", "lineage", "group", "et", "al", "and", "pl", "revised", "nov", "sensu", "lato",
"hybrid", "complex"),
tri_strings = c("\\sssp\\s", "\\sssp\\.\\s", "\\svar\\s",
"\\svar\\.\\s", "\\ssubsp\\.", "\\ssubspecies", "\\sform\\)",
"\\sform\\s", "\\sf\\.", "\\srace\\s", "\\srace\\)",
"\\sp\\.v\\."),
bi_strings = c("all\\ssubspecies", "\\ssp\\s", "\\ssp\\.\\s",
"\\sspecies", "\\sspp\\.\\s", "\\sspp\\s"),
atlas = c("Australia"),
tweak_species = TRUE,
return_taxonomy = TRUE,
limit = TRUE,
needed_ranks = c("species"),
overrides = NULL
)Dataframe with taxa_col. Can be NULL only if taxonomy_file
already exists.
Character or index. Name or index of column with taxa names.
Each unique taxa in this column will be queried against galah::search_taxa
and appear in the results list element lutaxain a column called
original_name
Character. File path to save results to. File type ignored. .parquet file used.
List with elements difftime and any column name from
taxonomy_file. If taxonomy_file already exists any column matches between
force_new and taxonomy_file, matching levels within that column will be
requeried. Likewise any original_name that has not been searched since
difftime will be requeried. Set either to NULL to ignore.
Character. Rows with regular expressions in
tolower(taxa_col) that match remove_taxa are removed (rows are removed).
Character. Text that matches remove_strings is
removed from the taxa_col before searching (text, not row, is removed).
Character. Text that matches non_name_strings is used to
remove non-names from original_names before a word count to indicate (guess)
if the original_name is trinomial (original_is_tri field in lutaxa).
Character. Text that matches these strings is
used to indicate if the original_name is trinomial or binomial. original_is
(bin)omial or (tri)nomial appear in the resulting lutaxa.
Character. Name of galah atlas to use.
Logical. If TRUE, a list is returned containing the
best match for each original_name in lutaxa and additional elements named
for their rank (see envClean::lurank) with unique rows for that rank. One
element per rank provided in needed_ranks
Logical. If TRUE the returned list will be limited to those
original_names in df
Character vector of ranks required in the returned list.
Can be "all" or any combination of ranks from envClean::lurank greater than
or equal to subspecies.
Used to override results returned by galah::search_taxa().
Dataframe with (at least) columns: taxa_col and taxa_to_search.
Can also contain any number of use_x columns where x is any of
kingdom, phylum, class, order, family, genus, species, subspecies, variety and form. A two step process then attempts
to find better results than if searched on taxa_col. Step 1 searches for
taxa_to_search instead of taxa_col. If any use_x columns are present,
step 2 then checks that the results from step 1 have a result at x. If not,
level x results will be taken from use_x.
Logical. If TRUE (default) and the returned species
column result ends in a full stop, the values returned in the species
column will be directly taken from the scientific_name column. See details.
Null or list (depending on return_taxonomy). Writes
taxonomy_file. taxa_col will be original_name in any outputs. Note that
taxa_col, as original_name, will have any quotes removed.
If list, then elements:
raw - the 'raw' results returned from galah::search_taxa(), tweaked
by: column rank is an ordered factor as per envClean::lurank;
rank_adj is a new column that will reflect the rank column unless rank is
less than subspecies, in which case it will be subspecies; and
original_is_(bi or tri) are new columns
needed_ranks - One element for each rank specified in needed_ranks.
lutaxa - dataframe. For each unique name in taxa_col, the best
taxa taxonomic bin to use, for each original_name, taking into
account each level of needed_ranks
original_name - unique values from taxa_col
match_type - directly from galah::search_taxa()
matched_rank - rank column from galah::search_taxa()
returned_rank - the rank of the taxa returned for each
original_name. This will never be lower than needed_rank but
may be higher than needed_rank if no match was available at
needed_rank. Use this 'rank' to filter bins in a cleaning
workflow
taxa - the best taxa available for original_name at
needed_rank, perhaps taking into account overrides
override - is the taxa the result of an override?
original_is_tri,original_is_bi - Experimental. Is the
original_name a trinomial or binomiail? Highlights cases where
the matched rank is > subspecies but the original_name is
probably a subspecies. Guesses are based on a word count after
removal of: not_names; numbers; punctuation; capitalised words
that are not the first word; and single letter 'words'.
bi_strings or tri_strings override the guess - flagging TRUE.
Note, clearly, this is only an (informed) guess at whether the
original_name is binomial or trinomial.
taxonomy - dataframe. For each taxa in lutaxa a row of
taxonomic hierarchy
The argument tweak_species replaces the galah::search_taxa() result in
the species column with the result in the scientific_name column. This
attempt to deal with instances where galah::search_taxa() returns odd
results in species but good results in scientific_name. e.g.
galah::search_taxa("Acacia sp. Small Red-leaved Wattle (J.B.Williams 95033)")
returns spec. in the species column but
Acacia sp. Small Red-leaved Wattle (J.B.Williams 95033) in the
scientific_name column
Previous envClean::make_taxonomy() function is still available via
envClean::make_gbif_taxonomy()
# setup
# library("envClean")
temp_file <- tempfile()
taxa_df <- tibble::tibble(taxa = c("Charadrius rubricollis"
, "Thinornis cucullatus"
, "Melithreptus gularis laetior"
, "Melithreptus gularis gularis"
, "Eucalyptus viminalis"
, "Eucalyptus viminalis cygnetensis"
, "Eucalyptus"
, "Charadrius mongolus all subspecies"
, "Bettongia lesueur Barrow and Boodie Islands subspecies"
, "Lagorchestes hirsutus Central Australian subspecies"
, "Perameles gunnii Victorian subspecies"
, "Pterostylis sp. Rock ledges (pl. 185, Bates & Weber 1990)"
, "Spyridium glabrisepalum"
, "Spyridium eriocephalum var. glabrisepalum"
, "Petrogale lateralis (MacDonnell Ranges race)"
, "Gehyra montium (revised)"
, "Korthalsella japonica f. japonica"
, "Galaxias sp. nov. 'Hunter'"
, "Some rubbish"
, "Senna artemisioides subsp x artemisioides"
, "Halosarcia sp. (NC)"
, "TERMITOIDAE sp." # 'epifamily'
)
)
# make taxonomy (returns list and writes taxonomy_file)
taxonomy <- make_taxonomy(df = taxa_df
, taxa_col = "taxa"
, taxonomy_file = temp_file
, needed_ranks = c("kingdom", "genus", "species", "subspecies")
)
#> Joining with `by = join_by(original_name)`
#> Matched 20 of 22 taxonomic search terms in selected atlas (Australia).
#> 2 unmatched search terms:
#> • "Galaxias sp. nov. Hunter", "Some rubbish"
#>
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d838e5192c.parquet
#> The following were completely unmatched: Galaxias sp. nov. Hunter and Some rubbish. Consider providing more taxonomic levels, or an override, for each unmatched taxa?
#> Joining with `by = join_by(original_name)`
#> Warning: There was 1 warning in `dplyr::filter()`.
#> ℹ In argument: `returned_rank == min(returned_rank)`.
#> Caused by warning in `min()`:
#> ! no non-missing arguments to min; returning Inf
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
taxonomy$raw
#> # A tibble: 22 × 20
#> original_name search_term scientific_name scientific_name_auth…¹
#> <chr> <chr> <chr> <chr>
#> 1 Bettongia lesueur Barrow … Bettongia … Bettongia lesu… NA
#> 2 Charadrius mongolus all s… Charadrius… Charadrius (Ch… Pallas, 1776
#> 3 Charadrius rubricollis Charadrius… Phalaropus lob… (Linnaeus, 1758)
#> 4 Eucalyptus Eucalyptus Eucalyptus L'Hér.
#> 5 Eucalyptus viminalis Eucalyptus… Eucalyptus vim… Labill.
#> 6 Eucalyptus viminalis cygn… Eucalyptus… Eucalyptus vim… Boomsma
#> 7 Galaxias sp. nov. Hunter Galaxias s… NA NA
#> 8 Gehyra montium (revised) Gehyra mon… Gehyra montium Storr, 1982
#> 9 Halosarcia sp. (NC) Halosarcia… Tecticornia Hook.f.
#> 10 Korthalsella japonica f. … Korthalsel… Korthalsella j… (Thunb.) Engl.
#> # ℹ 12 more rows
#> # ℹ abbreviated name: ¹scientific_name_authorship
#> # ℹ 16 more variables: taxon_concept_id <chr>, rank <ord>, match_type <chr>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, species <chr>, vernacular_name <chr>, stamp <dttm>,
#> # subspecies <chr>, rank_adj <ord>, original_is_tri <lgl>,
#> # original_is_bi <lgl>
taxonomy$kingdom
#> $lutaxa
#> # A tibble: 0 × 7
#> # ℹ 7 variables: original_name <chr>, match_type <chr>, matched_rank <ord>,
#> # returned_rank <ord>, taxa <chr>, original_is_tri <lgl>,
#> # original_is_bi <lgl>
#>
#> $taxonomy
#> # A tibble: 0 × 2
#> # ℹ 2 variables: taxa <chr>, kingdom <chr>
#>
taxonomy$genus
#> $lutaxa
#> # A tibble: 20 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Bettongia lesueu… exactMatch subspecies genus Bett… TRUE
#> 2 Charadrius mongo… higherMat… species genus Char… FALSE
#> 3 Charadrius rubri… exactMatch species genus Phal… FALSE
#> 4 Eucalyptus exactMatch genus genus Euca… FALSE
#> 5 Eucalyptus vimin… exactMatch species genus Euca… FALSE
#> 6 Eucalyptus vimin… exactMatch subspecies genus Euca… TRUE
#> 7 Gehyra montium (… canonical… species genus Gehy… FALSE
#> 8 Halosarcia sp. … exactMatch genus genus Tect… FALSE
#> 9 Korthalsella jap… higherMat… species genus Kort… TRUE
#> 10 Lagorchestes hir… canonical… species genus Lago… TRUE
#> 11 Melithreptus gul… exactMatch subspecies genus Meli… TRUE
#> 12 Melithreptus gul… exactMatch subspecies genus Meli… TRUE
#> 13 Perameles gunnii… exactMatch subspecies genus Pera… TRUE
#> 14 Petrogale latera… canonical… species genus Petr… TRUE
#> 15 Pterostylis sp. … exactMatch genus genus Pter… FALSE
#> 16 Senna artemisioi… higherMat… species genus Senna FALSE
#> 17 Spyridium erioce… exactMatch variety genus Spyr… TRUE
#> 18 Spyridium glabri… exactMatch variety genus Spyr… TRUE
#> 19 TERMITOIDAE sp. exactMatch NA order Blat… FALSE
#> 20 Thinornis cucull… exactMatch species genus Thin… FALSE
#> # ℹ 1 more variable: original_is_bi <lgl>
#>
#> $taxonomy
#> # A tibble: 16 × 7
#> taxa kingdom phylum class order family genus
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Bettongia Animalia Chordata Mammalia Diprotodontia Potoroi… Bett…
#> 2 Charadrius Animalia Chordata Aves Charadriiformes Charadr… Char…
#> 3 Phalaropus Animalia Chordata Aves Charadriiformes Scolopa… Phal…
#> 4 Eucalyptus Plantae Charophyta Equisetopsida Myrtales Myrtace… Euca…
#> 5 Gehyra Animalia Chordata Reptilia Squamata Gekkoni… Gehy…
#> 6 Tecticornia Plantae Charophyta Equisetopsida Caryophyllales Chenopo… Tect…
#> 7 Korthalsella Plantae Charophyta Equisetopsida Santalales Santala… Kort…
#> 8 Lagorchestes Animalia Chordata Mammalia Diprotodontia Macropo… Lago…
#> 9 Melithreptus Animalia Chordata Aves Passeriformes Melipha… Meli…
#> 10 Perameles Animalia Chordata Mammalia Peramelemorphia Peramel… Pera…
#> 11 Petrogale Animalia Chordata Mammalia Diprotodontia Macropo… Petr…
#> 12 Pterostylis Plantae Charophyta Equisetopsida Asparagales Orchida… Pter…
#> 13 Senna Plantae Charophyta Equisetopsida Fabales Fabaceae Senna
#> 14 Spyridium Plantae Charophyta Equisetopsida Rosales Rhamnac… Spyr…
#> 15 Blattodea Animalia Arthropoda Insecta Blattodea NA NA
#> 16 Thinornis Animalia Chordata Aves Charadriiformes Charadr… Thin…
#>
taxonomy$species
#> $lutaxa
#> # A tibble: 20 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Bettongia lesueu… exactMatch subspecies species Bett… TRUE
#> 2 Charadrius mongo… higherMat… species species Char… FALSE
#> 3 Charadrius rubri… exactMatch species species Phal… FALSE
#> 4 Eucalyptus exactMatch genus genus Euca… FALSE
#> 5 Eucalyptus vimin… exactMatch species species Euca… FALSE
#> 6 Eucalyptus vimin… exactMatch subspecies species Euca… TRUE
#> 7 Gehyra montium (… canonical… species species Gehy… FALSE
#> 8 Halosarcia sp. … exactMatch genus genus Tect… FALSE
#> 9 Korthalsella jap… higherMat… species species Kort… TRUE
#> 10 Lagorchestes hir… canonical… species species Lago… TRUE
#> 11 Melithreptus gul… exactMatch subspecies species Meli… TRUE
#> 12 Melithreptus gul… exactMatch subspecies species Meli… TRUE
#> 13 Perameles gunnii… exactMatch subspecies species Pera… TRUE
#> 14 Petrogale latera… canonical… species species Petr… TRUE
#> 15 Pterostylis sp. … exactMatch genus genus Pter… FALSE
#> 16 Senna artemisioi… higherMat… species species Senn… FALSE
#> 17 Spyridium erioce… exactMatch variety species Spyr… TRUE
#> 18 Spyridium glabri… exactMatch variety species Spyr… TRUE
#> 19 TERMITOIDAE sp. exactMatch NA order Blat… FALSE
#> 20 Thinornis cucull… exactMatch species species Thin… FALSE
#> # ℹ 1 more variable: original_is_bi <lgl>
#>
#> $taxonomy
#> # A tibble: 17 × 8
#> taxa kingdom phylum class order family genus species
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Bettongia lesueur Animalia Chordata Mammal… Dipr… Potor… Bett… Betton…
#> 2 Charadrius mongolus Animalia Chordata Aves Char… Chara… Char… Charad…
#> 3 Phalaropus lobatus Animalia Chordata Aves Char… Scolo… Phal… Phalar…
#> 4 Eucalyptus Plantae Charophyta Equise… Myrt… Myrta… Euca… NA
#> 5 Eucalyptus viminalis Plantae Charophyta Equise… Myrt… Myrta… Euca… Eucaly…
#> 6 Gehyra montium Animalia Chordata Reptil… Squa… Gekko… Gehy… Gehyra…
#> 7 Tecticornia Plantae Charophyta Equise… Cary… Cheno… Tect… NA
#> 8 Korthalsella japonica Plantae Charophyta Equise… Sant… Santa… Kort… Kortha…
#> 9 Lagorchestes hirsutus Animalia Chordata Mammal… Dipr… Macro… Lago… Lagorc…
#> 10 Melithreptus gularis Animalia Chordata Aves Pass… Melip… Meli… Melith…
#> 11 Perameles gunnii Animalia Chordata Mammal… Pera… Peram… Pera… Perame…
#> 12 Petrogale lateralis Animalia Chordata Mammal… Dipr… Macro… Petr… Petrog…
#> 13 Pterostylis Plantae Charophyta Equise… Aspa… Orchi… Pter… NA
#> 14 Senna artemisioides Plantae Charophyta Equise… Faba… Fabac… Senna Senna …
#> 15 Spyridium eriocephalum Plantae Charophyta Equise… Rosa… Rhamn… Spyr… Spyrid…
#> 16 Blattodea Animalia Arthropoda Insecta Blat… NA NA NA
#> 17 Thinornis cucullatus Animalia Chordata Aves Char… Chara… Thin… Thinor…
#>
taxonomy$subspecies
#> $lutaxa
#> # A tibble: 20 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Bettongia lesueu… exactMatch subspecies subspecies Bett… TRUE
#> 2 Charadrius mongo… higherMat… species species Char… FALSE
#> 3 Charadrius rubri… exactMatch species species Phal… FALSE
#> 4 Eucalyptus exactMatch genus genus Euca… FALSE
#> 5 Eucalyptus vimin… exactMatch species species Euca… FALSE
#> 6 Eucalyptus vimin… exactMatch subspecies subspecies Euca… TRUE
#> 7 Gehyra montium (… canonical… species species Gehy… FALSE
#> 8 Halosarcia sp. … exactMatch genus genus Tect… FALSE
#> 9 Korthalsella jap… higherMat… species species Kort… TRUE
#> 10 Lagorchestes hir… canonical… species species Lago… TRUE
#> 11 Melithreptus gul… exactMatch subspecies subspecies Meli… TRUE
#> 12 Melithreptus gul… exactMatch subspecies subspecies Meli… TRUE
#> 13 Perameles gunnii… exactMatch subspecies subspecies Pera… TRUE
#> 14 Petrogale latera… canonical… species species Petr… TRUE
#> 15 Pterostylis sp. … exactMatch genus genus Pter… FALSE
#> 16 Senna artemisioi… higherMat… species species Senn… FALSE
#> 17 Spyridium erioce… exactMatch variety subspecies Spyr… TRUE
#> 18 Spyridium glabri… exactMatch variety subspecies Spyr… TRUE
#> 19 TERMITOIDAE sp. exactMatch NA order Blat… FALSE
#> 20 Thinornis cucull… exactMatch species species Thin… FALSE
#> # ℹ 1 more variable: original_is_bi <lgl>
#>
#> $taxonomy
#> # A tibble: 19 × 9
#> taxa kingdom phylum class order family genus species subspecies
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Bettongia lesueur… Animal… Chord… Mamm… Dipr… Potor… Bett… Betton… Bettongia…
#> 2 Charadrius mongol… Animal… Chord… Aves Char… Chara… Char… Charad… NA
#> 3 Phalaropus lobatus Animal… Chord… Aves Char… Scolo… Phal… Phalar… NA
#> 4 Eucalyptus Plantae Charo… Equi… Myrt… Myrta… Euca… NA NA
#> 5 Eucalyptus vimina… Plantae Charo… Equi… Myrt… Myrta… Euca… Eucaly… NA
#> 6 Eucalyptus vimina… Plantae Charo… Equi… Myrt… Myrta… Euca… Eucaly… Eucalyptu…
#> 7 Gehyra montium Animal… Chord… Rept… Squa… Gekko… Gehy… Gehyra… NA
#> 8 Tecticornia Plantae Charo… Equi… Cary… Cheno… Tect… NA NA
#> 9 Korthalsella japo… Plantae Charo… Equi… Sant… Santa… Kort… Kortha… NA
#> 10 Lagorchestes hirs… Animal… Chord… Mamm… Dipr… Macro… Lago… Lagorc… NA
#> 11 Melithreptus gula… Animal… Chord… Aves Pass… Melip… Meli… Melith… Melithrep…
#> 12 Melithreptus gula… Animal… Chord… Aves Pass… Melip… Meli… Melith… Melithrep…
#> 13 Perameles gunnii … Animal… Chord… Mamm… Pera… Peram… Pera… Perame… Perameles…
#> 14 Petrogale lateral… Animal… Chord… Mamm… Dipr… Macro… Petr… Petrog… NA
#> 15 Pterostylis Plantae Charo… Equi… Aspa… Orchi… Pter… NA NA
#> 16 Senna artemisioid… Plantae Charo… Equi… Faba… Fabac… Senna Senna … NA
#> 17 Spyridium eriocep… Plantae Charo… Equi… Rosa… Rhamn… Spyr… Spyrid… Spyridium…
#> 18 Blattodea Animal… Arthr… Inse… Blat… NA NA NA NA
#> 19 Thinornis cuculla… Animal… Chord… Aves Char… Chara… Thin… Thinor… NA
#>
# query more taxa (results are added to taxonomy_file but only the new taxa are returned (default `limit = TRUE`)
more_taxa <- tibble::tibble(original_name = c("Amytornis whitei"
, "Amytornis striatus"
, "Amytornis modestus (North, 1902)"
, "Amytornis modestus modestus"
, "Amytornis modestus cowarie"
)
)
make_taxonomy(df = more_taxa
, taxonomy_file = temp_file
, needed_ranks = c("species")
)
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d838e5192c.parquet
#> The following were completely unmatched: Galaxias sp. nov. Hunter and Some rubbish. Consider providing more taxonomic levels, or an override, for each unmatched taxa?
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> $raw
#> # A tibble: 5 × 20
#> original_name search_term scientific_name scientific_name_auth…¹
#> <chr> <chr> <chr> <chr>
#> 1 Amytornis modestus (North,… Amytornis … Amytornis (Amy… (North, 1902)
#> 2 Amytornis modestus cowarie Amytornis … Amytornis (Amy… Black, 2016
#> 3 Amytornis modestus modestus Amytornis … Amytornis (Amy… (North, 1902)
#> 4 Amytornis striatus Amytornis … Amytornis (Mag… (Gould, 1840)
#> 5 Amytornis whitei Amytornis … Amytornis (Mag… Mathews, 1910
#> # ℹ abbreviated name: ¹scientific_name_authorship
#> # ℹ 16 more variables: taxon_concept_id <chr>, rank <ord>, match_type <chr>,
#> # kingdom <chr>, phylum <chr>, class <chr>, order <chr>, family <chr>,
#> # genus <chr>, species <chr>, vernacular_name <chr>, stamp <dttm>,
#> # subspecies <chr>, rank_adj <ord>, original_is_tri <lgl>,
#> # original_is_bi <lgl>
#>
#> $species
#> $species$lutaxa
#> # A tibble: 5 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Amytornis modestu… canonical… species species Amyt… FALSE
#> 2 Amytornis modestu… exactMatch subspecies species Amyt… TRUE
#> 3 Amytornis modestu… exactMatch subspecies species Amyt… TRUE
#> 4 Amytornis striatus exactMatch species species Amyt… FALSE
#> 5 Amytornis whitei exactMatch species species Amyt… FALSE
#> # ℹ 1 more variable: original_is_bi <lgl>
#>
#> $species$taxonomy
#> # A tibble: 3 × 8
#> taxa kingdom phylum class order family genus species
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Amytornis modestus Animalia Chordata Aves Passeriformes Maluri… Amyt… Amytor…
#> 2 Amytornis striatus Animalia Chordata Aves Passeriformes Maluri… Amyt… Amytor…
#> 3 Amytornis whitei Animalia Chordata Aves Passeriformes Maluri… Amyt… Amytor…
#>
#>
# no dataframe supplied - all results in taxonomy_file returned
make_taxonomy(taxonomy_file = temp_file
, needed_ranks = c("subspecies")
)
#> Joining with `by = join_by(original_name)`
#> $raw
#> original_name
#> 1 Amytornis modestus (North, 1902)
#> 2 Amytornis modestus cowarie
#> 3 Amytornis modestus modestus
#> 4 Amytornis striatus
#> 5 Amytornis whitei
#> 6 Bettongia lesueur Barrow and Boodie Islands subspecies
#> 7 Charadrius mongolus all subspecies
#> 8 Charadrius rubricollis
#> 9 Eucalyptus
#> 10 Eucalyptus viminalis
#> 11 Eucalyptus viminalis cygnetensis
#> 12 Galaxias sp. nov. Hunter
#> 13 Gehyra montium (revised)
#> 14 Halosarcia sp. (NC)
#> 15 Korthalsella japonica f. japonica
#> 16 Lagorchestes hirsutus Central Australian subspecies
#> 17 Melithreptus gularis gularis
#> 18 Melithreptus gularis laetior
#> 19 Perameles gunnii Victorian subspecies
#> 20 Petrogale lateralis (MacDonnell Ranges race)
#> 21 Pterostylis sp. Rock ledges (pl. 185, Bates & Weber 1990)
#> 22 Senna artemisioides subsp x artemisioides
#> 23 Some rubbish
#> 24 Spyridium eriocephalum var. glabrisepalum
#> 25 Spyridium glabrisepalum
#> 26 TERMITOIDAE sp.
#> 27 Thinornis cucullatus
#> search_term
#> 1 Amytornis modestus (North, 1902)
#> 2 Amytornis modestus cowarie
#> 3 Amytornis modestus modestus
#> 4 Amytornis striatus
#> 5 Amytornis whitei
#> 6 Bettongia lesueur Barrow and Boodie Islands subspecies
#> 7 Charadrius mongolus all subspecies
#> 8 Charadrius rubricollis
#> 9 Eucalyptus
#> 10 Eucalyptus viminalis
#> 11 Eucalyptus viminalis cygnetensis
#> 12 Galaxias sp. nov. Hunter
#> 13 Gehyra montium (revised)
#> 14 Halosarcia sp.
#> 15 Korthalsella japonica f. japonica
#> 16 Lagorchestes hirsutus Central Australian subspecies
#> 17 Melithreptus gularis gularis
#> 18 Melithreptus gularis laetior
#> 19 Perameles gunnii Victorian subspecies
#> 20 Petrogale lateralis (MacDonnell Ranges race)
#> 21 Pterostylis sp. Rock ledges (pl. 185, Bates & Weber 1990)
#> 22 Senna artemisioides subsp
#> 23 Some rubbish
#> 24 Spyridium eriocephalum var. glabrisepalum
#> 25 Spyridium glabrisepalum
#> 26 TERMITOIDAE
#> 27 Thinornis cucullatus
#> scientific_name
#> 1 Amytornis (Amytornis) modestus
#> 2 Amytornis (Amytornis) modestus cowarie
#> 3 Amytornis (Amytornis) modestus modestus
#> 4 Amytornis (Magnamytis) striatus
#> 5 Amytornis (Magnamytis) whitei
#> 6 Bettongia lesueur Barrow and Boodie Islands subspecies
#> 7 Charadrius (Charadrius) mongolus
#> 8 Phalaropus lobatus
#> 9 Eucalyptus
#> 10 Eucalyptus viminalis
#> 11 Eucalyptus viminalis subsp. cygnetensis
#> 12 <NA>
#> 13 Gehyra montium
#> 14 Tecticornia
#> 15 Korthalsella japonica
#> 16 Lagorchestes hirsutus
#> 17 Melithreptus (Eidopsarus) gularis gularis
#> 18 Melithreptus (Eidopsarus) gularis laetior
#> 19 Perameles gunnii Victorian subspecies
#> 20 Petrogale lateralis
#> 21 Pterostylis
#> 22 Senna artemisioides
#> 23 <NA>
#> 24 Spyridium eriocephalum var. glabrisepalum
#> 25 Spyridium eriocephalum var. glabrisepalum
#> 26 Termitoidae
#> 27 Thinornis cucullatus
#> scientific_name_authorship
#> 1 (North, 1902)
#> 2 Black, 2016
#> 3 (North, 1902)
#> 4 (Gould, 1840)
#> 5 Mathews, 1910
#> 6 <NA>
#> 7 Pallas, 1776
#> 8 (Linnaeus, 1758)
#> 9 L'Hér.
#> 10 Labill.
#> 11 Boomsma
#> 12 <NA>
#> 13 Storr, 1982
#> 14 Hook.f.
#> 15 (Thunb.) Engl.
#> 16 Gould, 1844
#> 17 (Gould, 1837)
#> 18 Gould, 1875
#> 19 <NA>
#> 20 Gould, 1842
#> 21 R.Br.
#> 22 (Gaudich. ex DC.) Randell
#> 23 <NA>
#> 24 J.M.Black
#> 25 J.M.Black
#> 26 <NA>
#> 27 (Vieillot, 1818)
#> taxon_concept_id
#> 1 https://biodiversity.org.au/afd/taxa/cfb67754-ed3f-4612-92bf-4753d23d49f0
#> 2 https://biodiversity.org.au/afd/taxa/a2736af9-dba4-4469-8439-9c367b1abb9f
#> 3 https://biodiversity.org.au/afd/taxa/6c201f56-6aba-47a7-95ce-4d0ba55cd55e
#> 4 https://biodiversity.org.au/afd/taxa/5b31a114-e88b-4b78-a2fe-c2fdc306dbdc
#> 5 https://biodiversity.org.au/afd/taxa/85b1ccbd-eefd-41b6-870b-cdbe452639cb
#> 6 ALA_DR22912_1262
#> 7 https://biodiversity.org.au/afd/taxa/fe772d84-8028-44b8-8530-c30a9112157e
#> 8 https://biodiversity.org.au/afd/taxa/9f562f99-aac8-4b16-b3c9-04a7eea35269
#> 9 https://id.biodiversity.org.au/taxon/apni/51738743
#> 10 https://id.biodiversity.org.au/taxon/apni/51290421
#> 11 https://id.biodiversity.org.au/node/apni/2914880
#> 12 <NA>
#> 13 https://biodiversity.org.au/afd/taxa/b84bd290-03f0-46d6-9cf7-e83600c60699
#> 14 https://id.biodiversity.org.au/taxon/apni/51433264
#> 15 https://id.biodiversity.org.au/node/apni/2916672
#> 16 https://biodiversity.org.au/afd/taxa/6e3213e1-c33b-45ae-9e05-6019211dd454
#> 17 https://biodiversity.org.au/afd/taxa/5ae49193-9e02-4a8d-a573-112cbf35c350
#> 18 https://biodiversity.org.au/afd/taxa/8742561c-c7e4-445c-97b6-ac63db433f6c
#> 19 ALA_DR22912_428
#> 20 https://biodiversity.org.au/afd/taxa/a610443a-5830-4d3c-a34a-092bf3adcb96
#> 21 https://id.biodiversity.org.au/taxon/apni/51726566
#> 22 https://id.biodiversity.org.au/taxon/apni/51285233
#> 23 <NA>
#> 24 https://id.biodiversity.org.au/node/apni/2887920
#> 25 https://id.biodiversity.org.au/node/apni/2887920
#> 26 https://biodiversity.org.au/afd/taxa/bf0614d9-26df-43f0-bfe8-b6d16d5d640a
#> 27 https://biodiversity.org.au/afd/taxa/1ebf8ec6-9aee-4b58-8789-0be73eb97b2f
#> rank match_type kingdom phylum class order
#> 1 species canonicalMatch Animalia Chordata Aves Passeriformes
#> 2 subspecies exactMatch Animalia Chordata Aves Passeriformes
#> 3 subspecies exactMatch Animalia Chordata Aves Passeriformes
#> 4 species exactMatch Animalia Chordata Aves Passeriformes
#> 5 species exactMatch Animalia Chordata Aves Passeriformes
#> 6 subspecies exactMatch Animalia Chordata Mammalia Diprotodontia
#> 7 species higherMatch Animalia Chordata Aves Charadriiformes
#> 8 species exactMatch Animalia Chordata Aves Charadriiformes
#> 9 genus exactMatch Plantae Charophyta Equisetopsida Myrtales
#> 10 species exactMatch Plantae Charophyta Equisetopsida Myrtales
#> 11 subspecies exactMatch Plantae Charophyta Equisetopsida Myrtales
#> 12 <NA> <NA> <NA> <NA> <NA> <NA>
#> 13 species canonicalMatch Animalia Chordata Reptilia Squamata
#> 14 genus exactMatch Plantae Charophyta Equisetopsida Caryophyllales
#> 15 species higherMatch Plantae Charophyta Equisetopsida Santalales
#> 16 species canonicalMatch Animalia Chordata Mammalia Diprotodontia
#> 17 subspecies exactMatch Animalia Chordata Aves Passeriformes
#> 18 subspecies exactMatch Animalia Chordata Aves Passeriformes
#> 19 subspecies exactMatch Animalia Chordata Mammalia Peramelemorphia
#> 20 species canonicalMatch Animalia Chordata Mammalia Diprotodontia
#> 21 genus exactMatch Plantae Charophyta Equisetopsida Asparagales
#> 22 species higherMatch Plantae Charophyta Equisetopsida Fabales
#> 23 <NA> <NA> <NA> <NA> <NA> <NA>
#> 24 variety exactMatch Plantae Charophyta Equisetopsida Rosales
#> 25 variety exactMatch Plantae Charophyta Equisetopsida Rosales
#> 26 <NA> exactMatch Animalia Arthropoda Insecta Blattodea
#> 27 species exactMatch Animalia Chordata Aves Charadriiformes
#> family genus species
#> 1 Maluridae Amytornis Amytornis modestus
#> 2 Maluridae Amytornis Amytornis modestus
#> 3 Maluridae Amytornis Amytornis modestus
#> 4 Maluridae Amytornis Amytornis striatus
#> 5 Maluridae Amytornis Amytornis whitei
#> 6 Potoroidae Bettongia Bettongia lesueur
#> 7 Charadriidae Charadrius Charadrius mongolus
#> 8 Scolopacidae Phalaropus Phalaropus lobatus
#> 9 Myrtaceae Eucalyptus <NA>
#> 10 Myrtaceae Eucalyptus Eucalyptus viminalis
#> 11 Myrtaceae Eucalyptus Eucalyptus viminalis
#> 12 <NA> <NA> <NA>
#> 13 Gekkonidae Gehyra Gehyra montium
#> 14 Chenopodiaceae Tecticornia <NA>
#> 15 Santalaceae Korthalsella Korthalsella japonica
#> 16 Macropodidae Lagorchestes Lagorchestes hirsutus
#> 17 Meliphagidae Melithreptus Melithreptus gularis
#> 18 Meliphagidae Melithreptus Melithreptus gularis
#> 19 Peramelidae Perameles Perameles gunnii
#> 20 Macropodidae Petrogale Petrogale lateralis
#> 21 Orchidaceae Pterostylis <NA>
#> 22 Fabaceae Senna Senna artemisioides
#> 23 <NA> <NA> <NA>
#> 24 Rhamnaceae Spyridium Spyridium eriocephalum
#> 25 Rhamnaceae Spyridium Spyridium eriocephalum
#> 26 <NA> <NA> <NA>
#> 27 Charadriidae Thinornis Thinornis cucullatus
#> vernacular_name stamp
#> 1 Thick-billed Grasswren 2025-06-17 07:25:31
#> 2 Cowarie Thick-billed Grasswren 2025-06-17 07:25:31
#> 3 Macdonnell Ranges Thick-billed Grasswren 2025-06-17 07:25:31
#> 4 Striated Grasswren 2025-06-17 07:25:31
#> 5 <NA> 2025-06-17 07:25:31
#> 6 Burrowing Bettong (barrow And Boodie Islands) 2025-06-17 07:25:29
#> 7 Lesser Sand Plover 2025-06-17 07:25:29
#> 8 Red-necked Phalarope 2025-06-17 07:25:29
#> 9 Studley Park Gum 2025-06-17 07:25:29
#> 10 Ribbon Gum 2025-06-17 07:25:29
#> 11 Rough-barked Manna-gum 2025-06-17 07:25:29
#> 12 <NA> 2025-06-17 07:25:29
#> 13 Centralian Dtella 2025-06-17 07:25:29
#> 14 Samphires 2025-06-17 07:25:29
#> 15 Jointed Mistletoe 2025-06-17 07:25:29
#> 16 Rufous Hare-wallaby 2025-06-17 07:25:29
#> 17 Black-chinned Honeyeater (eastern) 2025-06-17 07:25:29
#> 18 Golden-backed Honeyeater 2025-06-17 07:25:29
#> 19 Eastern Barred Bandicoot (mainland) 2025-06-17 07:25:29
#> 20 Black-footed Rock-wallaby 2025-06-17 07:25:29
#> 21 Greenhoods 2025-06-17 07:25:29
#> 22 Desert Cassia 2025-06-17 07:25:29
#> 23 <NA> 2025-06-17 07:25:29
#> 24 Macgillivray Spyridium 2025-06-17 07:25:29
#> 25 Macgillivray Spyridium 2025-06-17 07:25:29
#> 26 White Ants 2025-06-17 07:25:29
#> 27 Hooded Plover 2025-06-17 07:25:29
#> subspecies rank_adj
#> 1 <NA> species
#> 2 Amytornis modestus cowarie subspecies
#> 3 Amytornis modestus modestus subspecies
#> 4 <NA> species
#> 5 <NA> species
#> 6 Bettongia lesueur Barrow and Boodie Islands subspecies subspecies
#> 7 <NA> species
#> 8 <NA> species
#> 9 <NA> genus
#> 10 <NA> species
#> 11 Eucalyptus viminalis subsp. cygnetensis subspecies
#> 12 <NA> <NA>
#> 13 <NA> species
#> 14 <NA> genus
#> 15 <NA> species
#> 16 <NA> species
#> 17 Melithreptus gularis gularis subspecies
#> 18 Melithreptus gularis laetior subspecies
#> 19 Perameles gunnii Victorian subspecies subspecies
#> 20 <NA> species
#> 21 <NA> genus
#> 22 <NA> species
#> 23 <NA> <NA>
#> 24 Spyridium eriocephalum var. glabrisepalum subspecies
#> 25 Spyridium eriocephalum var. glabrisepalum subspecies
#> 26 <NA> <NA>
#> 27 <NA> species
#> original_is_tri original_is_bi
#> 1 FALSE TRUE
#> 2 TRUE FALSE
#> 3 TRUE FALSE
#> 4 FALSE TRUE
#> 5 FALSE TRUE
#> 6 TRUE FALSE
#> 7 FALSE TRUE
#> 8 FALSE TRUE
#> 9 FALSE FALSE
#> 10 FALSE TRUE
#> 11 TRUE FALSE
#> 12 FALSE TRUE
#> 13 FALSE TRUE
#> 14 FALSE FALSE
#> 15 TRUE FALSE
#> 16 TRUE FALSE
#> 17 TRUE FALSE
#> 18 TRUE FALSE
#> 19 TRUE FALSE
#> 20 TRUE FALSE
#> 21 FALSE TRUE
#> 22 FALSE TRUE
#> 23 FALSE TRUE
#> 24 TRUE FALSE
#> 25 TRUE FALSE
#> 26 FALSE FALSE
#> 27 FALSE TRUE
#>
#> $subspecies
#> $subspecies$lutaxa
#> # A tibble: 25 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <fct> <ord> <chr> <lgl>
#> 1 Amytornis modest… canonical… species species Amyt… FALSE
#> 2 Amytornis modest… exactMatch subspecies subspecies Amyt… TRUE
#> 3 Amytornis modest… exactMatch subspecies subspecies Amyt… TRUE
#> 4 Amytornis striat… exactMatch species species Amyt… FALSE
#> 5 Amytornis whitei exactMatch species species Amyt… FALSE
#> 6 Bettongia lesueu… exactMatch subspecies subspecies Bett… TRUE
#> 7 Charadrius mongo… higherMat… species species Char… FALSE
#> 8 Charadrius rubri… exactMatch species species Phal… FALSE
#> 9 Eucalyptus exactMatch genus genus Euca… FALSE
#> 10 Eucalyptus vimin… exactMatch species species Euca… FALSE
#> # ℹ 15 more rows
#> # ℹ 1 more variable: original_is_bi <lgl>
#>
#> $subspecies$taxonomy
#> # A tibble: 24 × 9
#> taxa kingdom phylum class order family genus species subspecies
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 Amytornis modestus Animal… Chord… Aves Pass… Malur… Amyt… Amytor… NA
#> 2 Amytornis modestu… Animal… Chord… Aves Pass… Malur… Amyt… Amytor… Amytornis…
#> 3 Amytornis modestu… Animal… Chord… Aves Pass… Malur… Amyt… Amytor… Amytornis…
#> 4 Amytornis striatus Animal… Chord… Aves Pass… Malur… Amyt… Amytor… NA
#> 5 Amytornis whitei Animal… Chord… Aves Pass… Malur… Amyt… Amytor… NA
#> 6 Bettongia lesueur… Animal… Chord… Mamm… Dipr… Potor… Bett… Betton… Bettongia…
#> 7 Charadrius mongol… Animal… Chord… Aves Char… Chara… Char… Charad… NA
#> 8 Phalaropus lobatus Animal… Chord… Aves Char… Scolo… Phal… Phalar… NA
#> 9 Eucalyptus Plantae Charo… Equi… Myrt… Myrta… Euca… NA NA
#> 10 Eucalyptus vimina… Plantae Charo… Equi… Myrt… Myrta… Euca… Eucaly… NA
#> # ℹ 14 more rows
#>
#>
# Try automatic overrides
auto_overrides <- make_unmatched_overrides(df = taxa_df
, taxa_col = "taxa"
, taxonomy = taxonomy
, target_rank = "species"
)
#> Joining with `by = join_by(original_name)`
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `res = purrr::map(...)`.
#> Caused by warning:
#> ! Unknown or uninitialised column: `scientificName`.
#> Joining with `by = join_by(original_name)`
#> Error in dplyr::select(dplyr::filter(dplyr::bind_rows(mget(ls(pattern = "^unmatched_")), .id = "note"), !is.na(!!rlang::ensym(taxa_col))), !!rlang::ensym(taxa_col), tidyr::any_of(tidyr::matches(unique(c(target_rank, "species")))), rank, scientific_name, kingdom, note): Can't select columns that don't exist.
#> ✖ Column `rank` doesn't exist.
# overrrides
overrides <- envClean::taxonomy_overrides
# C. rubricollis binned to Phalarope lobatus at species level!
taxonomy <- make_taxonomy(df = overrides
, taxonomy_file = temp_file
, needed_ranks = c("species", "subspecies")
)
#> Joining with `by = join_by(original_name)`
#> Matched 22 of 27 taxonomic search terms in selected atlas (Australia).
#> 5 unmatched search terms:
#> • "Aptenodes patagonicus", "Corybas", "Corybas" + 2 more
#>
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d838e5192c.parquet
#> The following were completely unmatched: Aptenodes patagonicus, Corybas X dentatus, Galaxias sp. nov. Hunter, Puffinis gravis, Puffinus griseus, Some rubbish and Corybas x dentatus. Consider providing more taxonomic levels, or an override, for each unmatched taxa?
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
taxonomy$species$lutaxa %>%
dplyr::filter(grepl("rubricollis", original_name))
#> # A tibble: 2 × 7
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Charadrius rubric… exactMatch species species Phal… FALSE
#> 2 Thinornis rubrico… higherMat… species species Thin… TRUE
#> # ℹ 1 more variable: original_is_bi <lgl>
# add in override - C. rubricollis is binned to T. cucullatus at species level
taxonomy <- make_taxonomy(df = overrides
, taxonomy_file = temp_file
, needed_ranks = c("species", "subspecies")
, overrides = overrides
)
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name, returned_rank)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d838e5192c.parquet
#> The following were completely unmatched: Galaxias sp. nov. Hunter and Some rubbish. Consider providing more taxonomic levels, or an override, for each unmatched taxa?
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
taxonomy$species$lutaxa %>%
dplyr::filter(grepl("rubricollis", original_name))
#> # A tibble: 2 × 8
#> original_name match_type matched_rank returned_rank taxa original_is_tri
#> <chr> <chr> <ord> <ord> <chr> <lgl>
#> 1 Charadrius rubric… exactMatch species species Thin… FALSE
#> 2 Thinornis rubrico… exactMatch subspecies species Thin… TRUE
#> # ℹ 2 more variables: original_is_bi <lgl>, override <lgl>
# tweak_species example
make_taxonomy(df = tibble::tibble(original_name = "Acacia sp. Small Red-leaved Wattle (J.B.Williams 95033)")
, tweak_species = FALSE
)$raw %>%
dplyr::select(original_name, scientific_name, species)
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d878804430.parquet
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> # A tibble: 1 × 3
#> original_name scientific_name species
#> <chr> <chr> <chr>
#> 1 Acacia sp. Small Red-leaved Wattle (J.B.Williams 9503… Acacia sp. Sma… NA
make_taxonomy(df = tibble::tibble(original_name = "Acacia sp. Small Red-leaved Wattle (J.B.Williams 95033)")
, tweak_species = TRUE
)$raw %>%
dplyr::select(original_name, scientific_name, species)
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> saving results to C:/temp/nige\RtmpEBQxW6\file34d87bf7640c.parquet
#> Joining with `by = join_by(original_name)`
#> Joining with `by = join_by(original_name)`
#> # A tibble: 1 × 3
#> original_name scientific_name species
#> <chr> <chr> <chr>
#> 1 Acacia sp. Small Red-leaved Wattle (J.B.Williams 9503… Acacia sp. Sma… NA
# clean up
rm(taxonomy)
unlist(paste0(temp_file, ".parquet"))
#> [1] "C:/temp/nige\\RtmpEBQxW6\\file34d838e5192c.parquet"