taxize offers interactive prompts when using get_*() functions (e.g., get_tsn()).
These prompts make it easy in interactive use to select choices when there are more
than one match found.
However, to make your code reproducible you don't want interactive prompts.
This vignette covers some options for programmatic name cleaning.
library("taxize")
When using get_*() functions programatically, you have a few options.
Normally, if you get more than one result, you get a prompt asking you to select which taxon you want.
get_tsn(searchterm = "Quercus b")
#> tsn target commonnames nameusage
#> 1 19298 Quercus beebiana not accepted
#> 2 507263 Quercus berberidifolia scrub oak accepted
#> 3 19300 Quercus bicolor swamp white oak accepted
#> 4 19303 Quercus borealis not accepted
#> 5 195131 Quercus borealis var. maxima not accepted
#> 6 195166 Quercus boyntonii Boynton's sand post oak accepted
#> 7 506533 Quercus brantii Brant's oak accepted
#> 8 195150 Quercus breviloba not accepted
#> 9 195099 Quercus breweri not accepted
#> 10 195168 Quercus buckleyi Texas oak accepted
#>
#> More than one TSN found for taxon 'Quercus b'!
#>
#> Enter rownumber of taxon (other inputs will return 'NA'):
#>
#> 1:
Instead, we can use the rows parameter to specify which records we want by number only (not by a name itself). Here, we want the first 3 records:
get_tsn(searchterm = 'Quercus b', rows = 1:3)
#> tsn target commonnames nameusage
#> 1 19298 Quercus beebiana not accepted
#> 2 19300 Quercus bicolor swamp white oak accepted
#> 3 19303 Quercus borealis not accepted
#>
#> More than one TSN found for taxon 'Quercus b'!
#>
#> Enter rownumber of taxon (other inputs will return 'NA'):
#>
#> 1:
However, you still get a prompt as there is more than one result.
Thus, for full programmatic usage, you can specify a single row, if you happen to know which one you want:
get_tsn(searchterm = 'Quercus b', rows = 3)
#> [1] "19303"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] TRUE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19303"
#> attr(,"class")
#> [1] "tsn"
In reality it is unlikely you'll know which row you want, unless perhaps you just want one result from each query, regardless of what it is.
A better fit for programmatic use are underscore methods. Each get_*() function
has a sister method with and trailing underscore, e.g., get_tsn() and get_tsn_().
get_tsn_(searchterm = "Quercus b")
#> $`Quercus b`
#> # A tibble: 5 x 4
#> tsn scientificName commonNames
#> <chr> <chr> <chr>
#> 1 19300 Quercus bicolor swamp white oak,ch<ea>ne bicolore
#> 2 195166 Quercus boyntonii Boynton's sand post oak,Boynton's oak
#> 3 195168 Quercus buckleyi Texas oak,Buckley's oak
#> 4 506533 Quercus brantii Brant's oak
#> 5 507263 Quercus berberidifolia scrub oak
#> # ... with 1 more variables: nameUsage <chr>
The result is a single data.frame for each taxon queried, which can be processed downstream with whatever logic is required in your workflow.
You can also combine rows parameter with underscore functions, as a single
number of a range of numbers:
get_tsn_(searchterm = "Quercus b", rows = 1)
#> $`Quercus b`
#> # A tibble: 1 x 4
#> tsn scientificName commonNames nameUsage
#> <chr> <chr> <chr> <chr>
#> 1 19300 Quercus bicolor swamp white oak,ch<ea>ne bicolore accepted
get_tsn_(searchterm = "Quercus b", rows = 1:2)
#> $`Quercus b`
#> # A tibble: 2 x 4
#> tsn scientificName commonNames nameUsage
#> <chr> <chr> <chr> <chr>
#> 1 19300 Quercus bicolor swamp white oak,ch<ea>ne bicolore accepted
#> 2 195166 Quercus boyntonii Boynton's sand post oak,Boynton's oak accepted
All get_*() functions have associated as.*() functions (e.g., get_tsn() and as.tsn()).
Many taxize functions use taxonomic identifier classes (S3 objects) that are the output
of get_*() functions. as.*() methods make it easy to make the required S3 taxonomic
identifier classes if you already know the identifier. For example:
Already a tsn, returns the same
as.tsn(get_tsn("Quercus douglasii"))
#> [1] "19322"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"
#> attr(,"class")
#> [1] "tsn"
numeric
as.tsn(c(19322, 129313, 506198))
#> [1] "19322" "129313" "506198"
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"multiple_matches")
#> [1] FALSE FALSE FALSE
#> attr(,"pattern_match")
#> [1] FALSE FALSE FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"
#> [2] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=129313"
#> [3] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=506198"
And you can do the same for character, or list inputs - depending on the data source.
The above as.tsn() examples have the parameter check = TRUE, meaning we ping the
data source web service to make sure the identifier exists. You can skip that check
if you like by setting check = FALSE, and the result is returned much faster:
as.tsn(c("19322","129313","506198"), check = FALSE)
#> [1] "19322" "129313" "506198"
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found" "found" "found"
#> attr(,"multiple_matches")
#> [1] FALSE FALSE FALSE
#> attr(,"pattern_match")
#> [1] FALSE FALSE FALSE
#> attr(,"uri")
#> [1] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"
#> [2] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=129313"
#> [3] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=506198"
With the output of as.*() methods, you can then proceed with other taxize functions.
Some functions in taxize are meant specifically for name cleaning. One of those
is gnr_resolve().
gnr_resolve() doesn't provide prompts as do get_*() functions, but instead
return data.frame's. So we don't face the same problem, and can use gnr_resolve()
in a programmatic workflow straight away.
spp <- names_list(rank = "species", size = 10)
gnr_resolve(names = spp, preferred_data_sources = 11)
#> user_supplied_name submitted_name
#> 1 Helichrysum candollei Helichrysum candollei
#> 2 Haworthia retusa Haworthia retusa
#> 3 Crypsinus bakeri Crypsinus bakeri
#> 4 Mangifera philippinensis Mangifera philippinensis
#> 5 Selaginella atirrensis Selaginella atirrensis
#> 6 Hymenostomum sullivanii Hymenostomum sullivanii
#> 7 Hymenostomum sullivanii Hymenostomum sullivanii
#> 8 Cytisus urumoffii Cytisus urumoffii
#> 9 Cytisus urumoffii Cytisus urumoffii
#> 10 Cytisus urumoffii Cytisus urumoffii
#> 11 Baptisia uniflora Baptisia uniflora
#> 12 Baptisia uniflora Baptisia uniflora
#> 13 Baptisia uniflora Baptisia uniflora
#> 14 Baptisia uniflora Baptisia uniflora
#> 15 Nephelium xerocarpum Nephelium xerocarpum
#> 16 Baccharis gnaphalioides Baccharis gnaphalioides
#> 17 Baccharis gnaphalioides Baccharis gnaphalioides
#> matched_name
#> 1 Helichrysum candollei (Bojer ex DC.) R.Vig. & Humbert
#> 2 Haworthia retusa (L.) Duval
#> 3 Crypsinus bakeri (Luerss.) Tag.
#> 4 Mangifera philippinensis Mukherji
#> 5 Selaginella atirrensis Hieron.
#> 6 Hymenostomum sullivanii C. Müller ex Geheeb, 1897
#> 7 Hymenostomum sullivanii C. Müller
#> 8 Cytisus urumoffii Davidov ex Stoj.
#> 9 Cytisus urumoffii Davidoff ex Stoyanoff
#> 10 Cytisus urumoffii Davidoff
#> 11 Baptisia uniflora Hook.
#> 12 Baptisia uniflora (Michx.) Nutt.
#> 13 Baptisia uniflora (Michx.) Sm.
#> 14 Baptisia uniflora Spreng.
#> 15 Nephelium xerocarpum (Bl.) Cambess.
#> 16 Baccharis gnaphalioides Spreng.
#> 17 Baccharis gnaphalioides DC.
#> data_source_title score
#> 1 GBIF Backbone Taxonomy 0.988
#> 2 GBIF Backbone Taxonomy 0.988
#> 3 GBIF Backbone Taxonomy 0.988
#> 4 GBIF Backbone Taxonomy 0.988
#> 5 GBIF Backbone Taxonomy 0.988
#> 6 GBIF Backbone Taxonomy 0.988
#> 7 GBIF Backbone Taxonomy 0.988
#> 8 GBIF Backbone Taxonomy 0.988
#> 9 GBIF Backbone Taxonomy 0.988
#> 10 GBIF Backbone Taxonomy 0.988
#> 11 GBIF Backbone Taxonomy 0.988
#> 12 GBIF Backbone Taxonomy 0.988
#> 13 GBIF Backbone Taxonomy 0.988
#> 14 GBIF Backbone Taxonomy 0.988
#> 15 GBIF Backbone Taxonomy 0.988
#> 16 GBIF Backbone Taxonomy 0.988
#> 17 GBIF Backbone Taxonomy 0.988
Some other functions in taxize use get_*() functions internally (e.g., classification()),
but you can can generally pass on parameters to the get_*() functions internally.
Let us know if you have ideas for better ways to do programmatic name cleaning at https://github.com/ropensci/taxize/issues or https://discuss.ropensci.org/ !