feat(concordance): add minor error (mE) metric#111
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Adds mE (minor error) to concordance() and concordance_from_tables() as defined by Wanger et al. (1999) / ISO 20776-2: proportion of intermediate (I) isolates genotypically predicted as resistant. Computed as count(I=1 & pred=1) / count(I=1) for the R outcome when an I column is present; NA for NWT (no intermediate ECOFF category). Closes AMRverse#109
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Summary
mE(minor error) toconcordance()andconcordance_from_tables(), as defined by Wanger et al. (1999) / ISO 20776-2count(I=1 & pred=1) / count(I=1)NAfor the NWT outcome (no intermediate ECOFF category) and when noIcolumn is presentconcordance_from_tables()now encodes a binaryIcolumn from the observed SIR calls so mE flows through the per-drugconcordance()call automatically, capturing true=I, predicted=R discordancesprint.amr_concordance()conditionally displaysmEonly when non-NACloses #109
Test plan
concordance()with a binary matrix containing anIcolumn: checkmEis computed and printed under the R outcomeconcordance()for NWT outcome: checkmEisNAand not printedconcordance()with noIcolumn: checkmEisNAconcordance_from_tables(): checkmEappears inmetricsfor drugs with intermediate isolates