AMR for R: Antimicrobial Resistance Analysis

Note: the rules of 'EUCAST Clinical Breakpoints v11.0 (2021)' will be added in the next release, to be expected in February/March 2021. New Functions get_episode() and is_new_episode() to determine (patient) episodes which are not necessarily based on microorganisms. The get_episode() function returns the index number of the episode per group, while the is_new_episode()function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode. They also support dplyrs grouping (i.e. using group_by()): library(dplyr) example_isolates %>% group_by(patient_id, hospital_id) %>% filter(is_new_episode(date, episode_days = 60)) Functions mo_is_gram_negative() and mo_is_gram_positive() as wrappers around mo_gramstain(). They always return TRUEor FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria. Function mo_is_intrinsic_resistant() to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020. Functions random_mic(), random_disk() and random_rsi() for random value generation. The functions random_mic() and random_disk() take microorganism names and antibiotic names as input to make generation more realistic. Changed New argument ampc_cephalosporin_resistance in eucast_rules() to correct for AmpC de-repressed cephalosporin-resistant mutants Interpretation of antimicrobial resistance - as.rsi(): Reference data used for as.rsi() can now be set by the user, using the reference_data argument. This allows for using own interpretation guidelines. The user-set data must have the same structure as rsi_translation. Better determination of disk zones and MIC values when running as.rsi() on a data.frame Fix for using as.rsi() on a data.frame in older R versions as.rsi() on a data.frame will not print a message anymore if the values are already clean R/SI values If using as.rsi() on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this Fix for using as.rsi() on a data.frame that only contains one column for antibiotic interpretations Some functions are now context-aware when used inside dplyr verbs, such as filter(), mutate() and summarise(). This means that then the data argument does not need to be set anymore. This is the case for the new functions: mo_is_gram_negative() mo_is_gram_positive() mo_is_intrinsic_resistant() ... and for the existing functions: first_isolate(), key_antibiotics(), mdro(), brmo(), mrgn(), mdr_tb(), mdr_cmi2012(), eucast_exceptional_phenotypes() # to select first isolates that are Gram-negative # and view results of cephalosporins and aminoglycosides: library(dplyr) example_isolates %>% filter(first_isolate(), mo_is_gram_negative()) %>% select(mo, cephalosporins(), aminoglycosides()) %>% as_tibble() For antibiotic selection functions (such as cephalosporins(), aminoglycosides()) to select columns based on a certain antibiotic group, the dependency on the tidyselect package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later): # above example in base R: example_isolates[which(first_isolate() & mo_is_gram_negative()), c("mo", cephalosporins(), aminoglycosides())] For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the typed package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined. Fix for set_mo_source(), that previously would not remember the file location of the original file Deprecated function p_symbol() that not really fits the scope of this package. It will be removed in a future version. See here for the source code to preserve it. Updated coagulase-negative staphylococci determination with Becker et al. 2020 (PMID 32056452), meaning that the species S. argensis, S. caeli, S. debuckii, S. edaphicus and S. pseudoxylosus are now all considered CoNS Fix for using argument reference_df in as.mo() and mo_*() functions that contain old microbial codes (from previous package versions) Fixed a bug where mo_uncertainties() would not return the results based on the MO matching score Fixed a bug where as.mo() would not return results for known laboratory codes for microorganisms Fixed a bug where as.ab() would sometimes fail Better tibble printing for MIC values Fix for plotting MIC values with plot() Added plot() generic to class LA-MRSA and CA-MRSA are now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g. mo_genus("LA-MRSA")will return "Staphylococcus" and mo_is_gram_positive("LA-MRSA") will return TRUE. Fix for printing class in tibbles when all values are NA Fix for mo_shortname() when the input contains NA If as.mo() takes more than 30 seconds, some suggestions will be done to improve speed Other All messages and warnings thrown by this package now break sentences on whole words More extensive unit tests Internal calls to options() were all removed in favour of a new internal environment pkg_env Improved internal type setting (among other things: replaced all sapply() calls with vapply()) Added CodeFactor as a continuous code review to this package: https://www.codefactor.io/repository/github/msberends/amr/ Added Dr. Rogier Schade as contributo