Automate Response at Prompt in R interactive

Question

Please see below my reference to a previous question asked along these lines.

I am running the library taxize in R. Taxize includes a function for getting a stable number associated with a scientific name, get_tsn().

I can run this in interactive mode or non-interactive mode so that I am either prompted or not, respectively, to choose among multiple hits.

Interactive:

> tax.num <- get_tsn("Acer rubrum", ask=TRUE)
Retrieving data for taxon 'Acer rubrum'
tsn      target                      commonNames      nameUsage
1  28728 Acer rubrum                 red maple        accepted
2  28730 Acer rubrum ssp. drummondii NA not           accepted
3 526853 Acer rubrum var. drummondii Drummond's maple accepted
...
More than one TSN found for taxon 'Acer rubrum'!
Enter rownumber of taxon (other inputs will return 'NA'):

Non-interactive:

> tax.num <- get_tsn("Acer rubrum", ask=TRUE)
Retrieving data for taxon 'Acer rubrum'
Warning message:
> 1 result; no direct match found

I need to run this library in interactive mode so that I do not get an empty result when there is more than one match. However, babysitting this script is totally unrealistic for the size of my data, which are in the millions of scientific names. Thus, I want to automate a response to the prompt so that the answer is always 1. This will be the right answer for probably 99% of cases and will ultimately still lead to the right answer downstream in 100% of cases for reasons that are probably beyond the scope of this question.

Thus, how can I automate the response to always be 1?

I looked at this question and tried modifying my code accordingly.

options(httr_oauth_cache=T)
tax.num <- get_tsn("Acer rubrum",ask=T)

However, this gave the same result shown for interactive mode above.

Your help is appreciated.

`taxize` has a vignette about using it programmatically: https://cran.r-project.org/web/packages/taxize/vignettes/name_cleaning.html — Nathan Werth, Jan 23 '18 at 19:32
@Nathan Werth Beautiful! Obviously that's the correct answer. Thank you. tax.num <- get_tsn_(searchterm = "Acer rubrum", rows = 1) works just fine! — 17th Lvl Botanist, Jan 23 '18 at 19:42

17th Lvl Botanist · Answer 1 · 2018-01-23T19:45:25.307

UPDATE: Ignore below. Obviously Nathan Werth posted the best answer in a comment above.

tax.num <- get_tsn_(searchterm = "Acer rubrum", rows = 1)

works wonderfully!

...

I decided to modify the source code to handle this. I suspect that there is a more desirable solution, but this one meets my needs.

Thus, in the file get_tsn.R from the source, I replaced the following block of code

      # prompt
      message("\n\n")
      print(tsn_df)
      message("\nMore than one TSN found for taxon '", x, "'!\n
      Enter rownumber of taxon (other inputs will return 'NA'):\n") 
      # prompt
      take <- scan(n = 1, quiet = TRUE, what = 'raw')

with

      take <- 1

I could have deleted other echoing to screen bits, that are unnecessary and now not true.

The revised function, which I tested using trace("get_tsn",edit=TRUE), returns as follows:

> print(tax.num)
[1] "28728"
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=28728"
attr(,"class")
[1] "tsn"

I will recompile and install it on Linux now with the edit for use with this particular project.

I still welcome other, better answers.

Automate Response at Prompt in R interactive

1 Answers1