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.
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("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('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('Quercus b', rows = 3)
#> ══ 1 queries ═══════════════
#> ✔ Found: Quercus b
#> ══ Results ═════════════════
#>
#> ● Total: 1
#> ● Found: 1
#> ● Not Found: 0
#> [1] "19303"
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] TRUE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19303"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_("Quercus b")
#> $`Quercus b`
#> # A tibble: 5 x 4
#> tsn scientificName commonNames nameUsage
#> <chr> <chr> <chr> <chr>
#> 1 19300 Quercus bicolor swamp white oak,chêne bicolore accepted
#> 2 195166 Quercus boyntonii Boynton's sand post oak,Boynton's oak accepted
#> 3 195168 Quercus buckleyi Texas oak,Buckley's oak accepted
#> 4 506533 Quercus brantii Brant's oak accepted
#> 5 507263 Quercus berberidifolia scrub oak acceptedThe 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:
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 queries ═══════════════
#> ✔ Found: Quercus douglasii
#> ══ Results ═════════════════
#>
#> ● Total: 1
#> ● Found: 1
#> ● Not Found: 0
#> [1] "19322"
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"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] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"
#> [2] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=129313"
#> [3] "https://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] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=19322"
#> [2] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=129313"
#> [3] "https://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(spp, preferred_data_sources = 11)
#> # A tibble: 14 x 5
#> user_supplied_na… submitted_name matched_name data_source_tit… score
#> * <chr> <chr> <chr> <chr> <dbl>
#> 1 Prestonia seeman… Prestonia seema… Prestonia seemanni… GBIF Backbone T… 0.988
#> 2 Stephanodaphne p… Stephanodaphne … Stephanodaphne per… GBIF Backbone T… 0.988
#> 3 Eriogonum compos… Eriogonum compo… Eriogonum composit… GBIF Backbone T… 0.988
#> 4 Eriogonum compos… Eriogonum compo… Eriogonum composit… GBIF Backbone T… 0.988
#> 5 Acaulon muticum Acaulon muticum Acaulon muticum (H… GBIF Backbone T… 0.988
#> 6 Acaulon muticum Acaulon muticum Acaulon muticum C.… GBIF Backbone T… 0.988
#> 7 Ranunculus subte… Ranunculus subt… Ranunculus subtect… GBIF Backbone T… 0.988
#> 8 Leucopogon pogon… Leucopogon pogo… Leucopogon pogonoc… GBIF Backbone T… 0.988
#> 9 Leucopogon pogon… Leucopogon pogo… Leucopogon pogonoc… GBIF Backbone T… 0.988
#> 10 Calanthe obrenif… Calanthe obreni… Calanthe obrenifor… GBIF Backbone T… 0.988
#> 11 Palaquium pierrei Palaquium pierr… Palaquium pierrei … GBIF Backbone T… 0.988
#> 12 Lithospermum cus… Lithospermum cu… Lithospermum cuspi… GBIF Backbone T… 0.988
#> 13 Evodia lucida Evodia lucida Euodia lucida (Miq… GBIF Backbone T… 0.75
#> 14 Evodia lucida Evodia lucida Euodia lucida (A.G… GBIF Backbone T… 0.75Some 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/ !