Search returns odd records

[pozsgaig]

Hi,
when I search for parasites of the fall armyworm, other Lepidoptera species appear among the target taxa (e.g. Helicoverpa zea). Also, when I run a second search on the vector of species resulted from the first search (thus, these become the source taxa now), in the result data frame species which I have not been queried appear.

first_round<-get_interactions_by_taxa(sourcetaxon = "Spodoptera frugiperda", interactiontype = "hasParasite")
first_round[grep("Lepidoptera", first_round$target_taxon_path), ]

In this case, the problem may be with the viruses since there seem to be no standard of reporting their names and some automated taxon search may pick up the Lepidoptera taxonomy if the word "virus" is not clearly included in the name - just guessing though.

second_round<-get_interactions_by_taxa(sourcetaxon = unique(first_round$target_taxon_name), interactiontype = "parasiteOf", otherkeys = list("limit" = 10000000, "skip" = 0))

second_round[second_round$source_taxon_name == "Chaetogaedia crebra",] # Does exist

first_round[first_round$target_taxon_name == "Chaetogaedia crebra",] # Does not exist
first_round[first_round$source_taxon_name == "Chaetogaedia crebra",] # Does not exist either

BUT
first_round[first_round$target_taxon_name == "Tachinidae",] # Does exist

So, I believe, this is not a bug, the hits are merely there because they are under a higher taxon which was included in the search. Is there, however, any way to limit the results to the exact terms only?

R version 4.2.1 (2022-06-23 ucrt) rglobi 0.2.28
Thanks,
Gabor

[jhpoelen]

@pozsgaig Hi Gabor - Thanks for your detailed message! I believe you are mentioning various things, and I'll start with the last one.

So, I believe, this is not a bug, the hits are merely there because they are under a higher taxon which was included in the search. Is there, however, any way to limit the results to the exact terms only?

You can disable taxonomic inference by and do exact matches only by using the excludeChildTaxa option.

e.g.,

> rglobi::get_interactions_by_taxa(sourcetaxon = "Aves", interactiontype = "hasParasite", otherkeys = list("limit" = 10))$source_taxon_name
 [1] "Aimophila carpalis" "Aimophila carpalis" "Aimophila carpalis"           
 [4] "Aimophila carpalis" "Aimophila carpalis" "Aimophila carpalis"
 [7] "Aimophila carpalis" "Aimophila carpalis" "Aimophila carpalis"
[10] "Aimophila carpalis"

whereas,

> rglobi::get_interactions_by_taxa(sourcetaxon = "Aves", interactiontype = "hasParasite", otherkeys = list("limit" = 10, "excludeChildTaxa" = T))$source_taxon_name
 [1] "Aves" "Aves" "Aves" "Aves" "Aves" "Aves" "Aves" "Aves" "Aves" "Aves" 

So, excludeChildTaxa is a way of saying only include exact matches and don't do any taxonomic tricks.

Is that helpful?

-jorrit

ps. To help expedite these kinds of issues, it would help me (and probably others) to file one specific issue per issue, and include a description of the unexpected behavior in the title.

For instance, "rglobi claims that Donald Duck ate Mickey Mouse, even through Jane Doe claims that Donald Duck is a vegetarian" followed by a recipe to reproduce the results, including the received output.

Curious to hear your thoughts about the issue filing best practice above.

[pozsgaig]

@jhpoelen Hi Jorrit,
That's exactly what I was looking for.
Sure, I can file the other issue separately. Though, due to the multi-line output, the outputs are not always feasible to show.
Gabor

[jhpoelen]

@pozsgaig glad I was able to help.

Sure, I can file the other issue separately. Though, due to the multi-line output, the outputs are not always feasible to show.

Thank you! I can see your points about the multiline output. I try to put stuff in a file is there's too many results, and only include the head (top 10) results in the issue to make it easier to read the narrative.

By the way - Would you like to contribute an example from your work in the rglobi vignette to help our future selves remember all this? You can find the vignette at https://github.com/ropensci/rglobi/blob/main/vignettes/rglobi_vignette.Rmd .