eucast_rules() throws an error about amr

[msberends]

Thanks for using the package! I think this was fixed in our previous version, v1.3.0.

Could you try again by running install.packages("AMR"), restart R and try again?

[msberends]

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[msberends]

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")

[nrkoehler]

I'm still getting the same error message when using AMR version 1.3

  a <- data.frame(mo = c("Staphylococcus aureus",
                         "Enterococcus faecalis",
                         "Escherichia coli",
                         "Klebsiella pneumoniae",
                         "Pseudomonas aeruginosa"),
                  VAN = "-",       # Vancomycin
                  AMX = "-",       # Amoxicillin
                  COL = "-",       # Colistin
                  CAZ = "-",       # Ceftazidime
                  CXM = "-",       # Cefuroxime
                  PEN = "S",       # Benzylpenicillin
                  FOX = "S",       # Cefoxitin
                  stringsAsFactors = FALSE)
  
  b <- eucast_rules(a)

NOTE: Using column mo as input for col_mo.
NOTE: Auto-guessing columns suitable for analysis...OK.
NOTE: Reliability would be improved if these antimicrobial results would be available too: amoxicillin/clavulanic acid (AMC), amikacin (AMK), ampicillin (AMP), azithromycin (AZM), azlocillin (AZL), aztreonam (ATM), cefaloridine (RID), cefepime (FEP), cefotaxime (CTX), cephradine (CED), ceftriaxone (CRO), chloramphenicol (CHL), ciprofloxacin (CIP), clarithromycin (CLR), clindamycin (CLI), flucloxacillin (FLC), cefazolin (CZO), daptomycin (DAP), doxycycline (DOX), ertapenem (ETP), erythromycin (ERY), fosfomycin (FOS), fusidic acid (FUS), gentamicin (GEN), imipenem (IPM), kanamycin (KAN), levofloxacin (LVX), lincomycin (LIN), linezolid (LNZ), meropenem (MEM), mezlocillin (MEZ), minocycline (MNO), moxifloxacin (MFX), nalidixic acid (NAL), neomycin (NEO), netilmicin (NET), nitrofurantoin (NIT), norfloxacin (NOR), novobiocin (NOV), ofloxacin (OFX), oxacillin (OXA), piperacillin (PIP), piperacillin/tazobactam (TZP), polymyxin B (PLB), pristinamycin (PRI), quinupristin/dalfopristin (QDA), rifampicin (RIF), roxithromycin (RXT), sisomicin (SIS), teicoplanin (TEC), tetracycline (TCY), ticarcillin (TIC), tigecycline (TGC), tobramycin (TOB), trimethoprim (TMP), trimethoprim/sulfamethoxazole (SXT)
Fehler in value[3L] :
ungültiger regulärer Ausdruck '^(abbotic|abboticin|abdizide|abelcet|abelecet|abomacetin|acetohmt|acetylspiramycin|acideclavulanique|acidefusidique|acidoclavulanico|acidofusidico|acidomandelico|acidumclavulanicum|acidumfusidicum|acillin|acneryne|acnesol|acromona|acronize|actilin|actiline|actimoxi|aczone|adesulfonesodium|adobacillin|advocin|aeroquin|aethambutolum|aethionamidum|aetina|aetiva|aizumycin|aknecordeslosung|aknedermerygel|aknemycin|alcephin|alcobon|alconcilox|aldapsone|aldesulfonasodica|aldesulfone|aldesulfonesodique|aldesulfonesodium|alenfral|alexin|alfacet|alficetyn|alflucoz|alfumet|aliporina|almitil|almondacid|alsporin|altacef|ambisome|amblosin|ambofen|ambrocef|ambylan|amcill|amdinocillin|amfipen|amfipenv|amfotericinab|amicacin|amidazin|amidazine|amikacillin|amikacin|amikacinbase|amikacindihydrate|amikacinsulfate|amikacina|amikacine|amikacinum|amikavet|amikin|amiklin|amikozit|aminodeoxykanamycin|aminoform|aminoformaldehyde|aminopar|aminosalicylic|aminosalicylicaci

My session info:

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] AMR_1.3.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lubridate_1.7.9 crayon_1.3.4 dplyr_1.0.2 R6_2.4.1
[6] lifecycle_0.2.0 magrittr_1.5 pillar_1.4.6 rlang_0.4.7 rstudioapi_0.11
[11] effectr_0.20.10.06 vctrs_0.3.4 generics_0.0.2 ellipsis_0.3.1 tools_4.0.2
[16] glue_1.4.2 purrr_0.3.4 yaml_2.2.1 compiler_4.0.2 pkgconfig_2.0.3
[21] tidyselect_1.1.0 tibble_3.0.3

[msberends]

True, but 1.4.0 was released today 😃

Might not come up in your updated packages list until tomorrow, so please let me know if you still get this after you’ve installed the newest release.

[nrkoehler]

Oh, sorry. I didn't notice. :-) I will check it out now.

[nrkoehler]

It works just fine. Thanks a lot!

[msberends]

Great! Enjoy!