first isolates function does not take untested isolates into account about amr HOT 5 CLOSED

That is a great suggestion! I was just done writing when I saw this. It's a small code change, so here it is a new argument of the first_isolate() function:

include_untested_rsi
logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use include_untested_rsi = FALSE to always return FALSE for such rows. This checks the data set for columns of class <rsi> and consequently requires transforming columns with antibiotic results using as.rsi() first.

Still testing if it always work, then I'll upload it 🙂

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Until then (for the AMR package in dplyr-free code since dplyr is not a strict dependency):

    rsi_all_NA <- which(unname(vapply(FUN.VALUE = logical(1), 
                                      as.data.frame(t(x[, is.rsi(x), drop = FALSE])),
                                      function(rsi_values) all(is.na(rsi_values)))))
    x[rsi_all_NA, "first"] <- FALSE

So x is the data set and "first" is the column name created after first_isolate().

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thanks, sounds like a very good fix!

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(this is an automated reply)

The development version nows contains the fix to this issue. You can try the latest version yourself using:

install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")

Or you could wait until we release a new version to CRAN (which won't be long) 🙂

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Fix released to official R repository

Just a small notice: we released a new software version, containing the fix to this issue. Please update your version using either the user interface of your software, or by running:

install.packages("AMR")

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