Claude 1d48012355 eucast_rules(): add add_if_missing argument to control NA imputation (#259) ...

When `add_if_missing = FALSE`, rules are only applied to cells that already
contain an SIR value; `NA` cells are left untouched. This is useful with
`overwrite = TRUE` to update reported results without imputing values for
drugs that were not tested.

https://claude.ai/code/session_01Nucc8nXGLqNUjtuC9GrhTc

2026-03-09 20:00:06 +00:00

..

aa_amr-package.R

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00

aa_globals.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

aa_helper_functions.R

(v3.0.1.9031) fix MDRO for non-RStudio terminal

2026-03-08 11:30:18 +01:00

aa_helper_pm_functions.R

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

aa_options.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

ab_from_text.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

ab_property.R

(v3.0.1.9028) fix unique CIDs

2026-03-06 18:53:42 +01:00

ab.R

(v3.0.1.9026) fix ab_group(NA)

2026-03-06 12:41:27 +01:00

age.R

(v3.0.0.9011) allow names for age_groups()

2025-07-17 19:32:46 +02:00

amr_selectors.R

(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

2026-03-09 11:57:36 +01:00

antibiogram.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

atc_online.R

(v3.0.1.9005) re-add tidymodels implementation

2025-12-21 12:19:43 +01:00

av_from_text.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

av_property.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

av.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

availability.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

bug_drug_combinations.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

count.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

custom_antimicrobials.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

custom_eucast_rules.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

custom_mdro_guideline.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

custom_microorganisms.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

data.R

(v3.0.1.9007) fix #246

2026-01-06 23:08:50 +01:00

disk.R

(v3.0.1.9018) fixes #249

2026-01-16 10:57:03 +01:00

export_biosample.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

first_isolate.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

g.test.R

AMR v3.0\!

2025-06-02 12:11:00 +02:00

get_episode.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

ggplot_pca.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

ggplot_sir.R

(v3.0.0.9015) plotting fix

2025-07-19 14:06:36 +02:00

guess_ab_col.R

(v2.1.1.9288) mdro fix

2025-06-01 15:35:04 +02:00

interpretive_rules.R

eucast_rules(): add add_if_missing argument to control NA imputation (#259)

2026-03-09 20:00:06 +00:00

italicise_taxonomy.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

join_microorganisms.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

key_antimicrobials.R

(v3.0.1.9020) unit test fixes

2026-02-09 13:16:36 +01:00

kurtosis.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

like.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

mdro.R

(v3.0.1.9032) fix unit tests

2026-03-08 20:36:15 +01:00

mean_amr_distance.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

mic.R

mdro(): infer base drug resistance from drug+inhibitor combination co… (#263)

2026-03-07 18:06:55 +01:00

mo_matching_score.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

mo_property.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

mo_source.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

mo.R

(v3.0.1.9027) Fixes #252 and add documentation update regarding #253

2026-03-06 13:10:33 +01:00

pca.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

plotting.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

proportion.R

(v3.0.1.9021) add guideline to resistance() and susceptibility()

2026-02-12 20:34:06 +01:00

random.R

(v3.0.0.9004) random mic fix

2025-06-13 16:12:28 +02:00

resistance_predict.R

(v2.1.1.9279) fix documentation, add foreign S3 exports to functions

2025-05-16 16:55:29 +02:00

sir_calc.R

(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

2026-02-08 23:15:40 +01:00

sir_df.R

(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

2025-07-17 17:05:41 +02:00

sir.R

mdro(): infer base drug resistance from drug+inhibitor combination co… (#263)

2026-03-07 18:06:55 +01:00

skewness.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

sysdata.rda

(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

2026-03-09 11:57:36 +01:00

tidymodels.R

(v3.0.1.9005) re-add tidymodels implementation

2025-12-21 12:19:43 +01:00

top_n_microorganisms.R

(v2.1.1.9253) parallel computing

2025-04-26 15:47:00 +02:00

translate.R

(v3.0.1.9015) fix translations

2026-01-08 10:21:48 +01:00

vctrs.R

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

whocc.R

(v2.1.1.9236) documentation

2025-04-12 11:46:42 +02:00

zz_deprecated.R

(v2.1.1.9287) fix antibiotics

2025-06-01 12:17:47 +02:00

zzz.R

(v3.0.1.9022) add ceftibuten/avibactam (CTA), kasugamycin (KAS), ostreogrycin (OST), thiostrepton (THS), xeruborbactam (XER), zorbamycin (ZOR)

2026-03-03 15:41:08 +01:00