msberends/AMR: v0.4.0

0.4.0 New The data set microorganisms now contains all microbial taxonomic data from ITIS (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set microorganisms.old contains all previously known taxonomic names from those kingdoms. New functions based on the existing function mo_property: Taxonomic names: mo_phylum, mo_class, mo_order, mo_family, mo_genus, mo_species, mo_subspecies Semantic names: mo_fullname, mo_shortname Microbial properties: mo_type, mo_gramstain Author and year: mo_ref They also come with support for German, Dutch, French, Italian, Spanish and Portuguese: mo_gramstain("E. coli") # [1] "Gram negative" mo_gramstain("E. coli", language = "de") # German # [1] "Gramnegativ" mo_gramstain("E. coli", language = "es") # Spanish # [1] "Gram negativo" mo_fullname("S. group A", language = "pt") # Portuguese # [1] "Streptococcus grupo A" Furthermore, former taxonomic names will give a note about the current taxonomic name: mo_gramstain("Esc blattae") # Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010) # [1] "Gram negative" Functions count_R, count_IR, count_I, count_SI and count_S to selectively count resistant or susceptible isolates Extra function count_df (which works like portion_df) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables Function is.rsi.eligible to check for columns that have valid antimicrobial results, but do not have the rsi class yet. Transform the columns of your raw data with: data %>% mutate_if(is.rsi.eligible, as.rsi) Functions as.mo and is.mo as replacements for as.bactid and is.bactid (since the microoganisms data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The as.mo function determines microbial IDs using Artificial Intelligence (AI): as.mo("E. coli") # [1] B_ESCHR_COL as.mo("MRSA") # [1] B_STPHY_AUR as.mo("S group A") # [1] B_STRPTC_GRA And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items: thousands_of_E_colis <- rep("E. coli", 25000) microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s") # Unit: seconds # min median max neval # 0.01817717 0.01843957 0.03878077 100 Added parameter reference_df for as.mo, so users can supply their own microbial IDs, name or codes as a reference table Renamed all previous references to bactid to mo, like: Column names inputs of EUCAST_rules, first_isolate and key_antibiotics Column names of datasets microorganisms and septic_patients All old syntaxes will still work with this version, but will throw warnings Function labels_rsi_count to print datalabels on a RSI ggplot2 model Functions as.atc and is.atc to transform/look up antibiotic ATC codes as defined by the WHO. The existing function guess_atc is now an alias of as.atc. Function ab_property and its aliases: ab_name, ab_tradenames, ab_certe, ab_umcg and ab_trivial_nl Introduction to AMR as a vignette Removed clipboard functions as it violated the CRAN policy Renamed septic_patients$sex to septic_patients$gender Changed Added three antimicrobial agents to the antibiotics data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05) Added 163 trade names to the antibiotics data set, it now contains 298 different trade names in total, e.g.: ab_official("Bactroban") # [1] "Mupirocin" ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin" ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen")) # [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05" For first_isolate, rows will be ignored when there's no species available Function ratio is now deprecated and will be removed in a future release, as it is not really the scope of this package Fix for as.mic for values ending in zeroes after a real number Small fix where B. fragilis would not be found in the microorganisms.umcg data set Added prevalence column to the microorganisms data set Added parameters minimum and as_percent to portion_df Support for quasiquotation in the functions series count_* and portions_*, and n_rsi. This allows to check for more than 2 vectors or columns. septic_patients %>% select(amox, cipr) %>% count_IR() # which is the same as: septic_patients %>% count_IR(amox, cipr) septic_patients %>% portion_S(amcl) septic_patients %>% portion_S(amcl, gent) septic_patients %>% portion_S(amcl, gent, pita) Edited ggplot_rsi and geom_rsi so they can cope with count_df. The new fun parameter has value portion_df at default, but can be set to count_df. Fix for ggplot_rsi when the ggplot2 package was not loaded Added datalabels function labels_rsi_count to ggplot_rsi Added possibility to set any parameter to geom_rsi (and ggplot_rsi) so you can set your own preferences Fix for joins, where predefined suffices would not be honoured Added parameter quote to the freq function Added generic function diff for frequency tables Added longest en shortest character length in the frequency table (freq) header of class character Support for types (classes) list and matrix for freq my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2)) freq(my_matrix) For lists, subsetting is possible: my_list = list(age = septic_patients$age, gender = septic_patients$gender) my_list %>% freq(age) my_list %>% freq(gender) Other More unit tests to ensure better integrity of function