Add alpha argument for CI width calculation #215

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1. lenthomas commented on Oct 16, 2025

   

   lenthomas

   on Oct 16, 2025

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   I created a branch for this request - branch Issue_215. In that, I added an argument conf_level to the ds function. I used this argument name as it's what's used in other packages that produce confidence intervals such as PropCIs (well, they use conf.level but our convention is to use an underscore). Here's some code that exercises that argument:

   library(Distance)
   data(book.tee.data)
   tee.data <- subset(book.tee.data$book.tee.dataframe, observer==1)
   ds.model <- ds(tee.data, 4)
   summary(ds.model)
   
   region <- book.tee.data$book.tee.region
   samples <- book.tee.data$book.tee.samples
   obs <- book.tee.data$book.tee.obs
   
   ds.dht.model <- ds(tee.data, 4, region_table=region,
                      sample_table=samples, obs_table=obs, conf_level=0.8)
   summary(ds.dht.model)
   

   @erex Let me know what you think and if okay I'll merge with the main branch. Thanks for making it so easy to work out what to do!
2. lenthomas

   self-assigned this

   on Oct 16, 2025
3. lenthomas

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   on Oct 16, 2025
4. erex commented on Oct 17, 2025

   

   erex

   on Oct 17, 2025

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   yes, this all looks good; argument is even added to documentation.

   Vaguely related to this is how user specifies CI desires for bootdht. The function summary.dht_bootstrap (note interesting coding convention use of . and _) asks the user to specify $\alpha$ rather than $1-\alpha$ as is done with dht. But that might be for another day.
5. lenthomas commented on Oct 17, 2025

   

   lenthomas

   on Oct 17, 2025

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   Thanks for pointing that out. How about I create an alpha argument for ds that has no default, so has no effect if you don't use it, but if you do it takes precidence over conf_level? That way the user can use either. (I could also create a conf_level argument for summary.dht_bootstrap.)

   The mixture of dot and underscore in summary.dht_bootstrap is because we're using S3 classes in the Distance package and the dot is how you tell R that this function is a summary function for the dht_bootstrap class. Clunky, but S3 has been around for yonks and that's how it works.
6. erex commented on Oct 17, 2025

   

   erex

   on Oct 17, 2025

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   I'm relaxed about what you do with alpha and conf_level. Would be nice if there was consistency between functions within our packages.
7. lenthomas commented on Oct 17, 2025

   

   lenthomas

   on Oct 17, 2025

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   Indeed, with this in mind I added an alpha argument to ds, tested, and merged in with the main branch. I didn't add conf_level to dht_bootstrap as that's complicated enough as is, so I thought I'd leave it. I'll close this issue now - please can you pass back info about the new feature to your workshop participant.
8. lenthomas

   closed this as completedon Oct 17, 2025
9. erex

   reopened this on Oct 17, 2025
10. erex commented on Oct 17, 2025

    

    erex

    on Oct 17, 2025

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    Don't think this is closed yet, see my comment in pull request #217 #217

    Something not quite right about roxygen I'm guessing. You changed ds.R, but those changes did not propagate into ds.Rd in the documentation. Github actions noticed this and complained the two files are inconsistent.
11. lenthomas commented on Oct 17, 2025

    

    lenthomas

    on Oct 17, 2025

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    Thanks, clearly I am out of date with this stuff. I ran devtools::document() and pushed the new .Rd. Should all be fine now.
12. lenthomas

    closed this as completedon Oct 17, 2025