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AMR/NEWS.md

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0.3.0.90xx (latest development version)

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.

  • Aliases for 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.

    They also come with support for German, Dutch, French, Italian, Spanish and Portuguese, and it defaults to the systems locale:

    mo_gramstain("E. coli")
# [1] "Gram negative"
mo_gramstain("E. coli", language = "de") # "de" = Deutsch / German
# [1] "Gramnegativ"
mo_gramstain("E. coli", language = "es") # "es" = Español / Spanish
# [1] "Gram negativo"
mo_fullname("S. group A") # when run on a on a Portuguese system
# [1] "Streptococcus grupo A"

    Furthermore, old taxonomic names kan easily be looked up and give a note about the taxonomic change:

    mo_fullname("Pseudomonas facilis")
# Note: 'Pseudomonas facilis' was renamed to 'Acidovorax facilis' by Willems et al. in 1990
# [1] "Acidovorax facilis"

  • 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] ESCCOL
as.mo("MRSA")
# [1] STAAUR
as.mo("S group A")
# [1] STCGRA

    And with great speed too - on a quite regular Linux server from 2007 it takes us 0.009 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
#  0.00861352  0.008774335  0.01952958    100

  • 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

Changed

  • Added almost 200 microorganisms to the microorganisms data set and removed the few viruses it contained
  • 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 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, sex), ncol = 2))
freq(my_matrix)
    For lists, subsetting is possible: 
    my_list = list(age = septic_patients$age, sex = septic_patients$sex)
my_list %>% freq(age)
my_list %>% freq(sex)

Other

  • More unit tests to ensure better integrity of functions

0.3.0 (latest stable version)

Published on CRAN: 2018-08-14

New

  • BREAKING: rsi_df was removed in favour of new functions portion_R, portion_IR, portion_I, portion_SI and portion_S to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old rsi function. The old function still works, but is deprecated.
    • New function portion_df to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables
  • BREAKING: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call key antibiotics) to include more first isolates (afterwards called first weighted isolates) are now as follows:
    • Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole
    • Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin
    • Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem
  • Support for ggplot2
    • New functions geom_rsi, facet_rsi, scale_y_percent, scale_rsi_colours and theme_rsi
    • New wrapper function ggplot_rsi to apply all above functions on a data set:
      • septic_patients %>% select(tobr, gent) %>% ggplot_rsi will show portions of S, I and R immediately in a pretty plot
      • Support for grouped variables, see ?ggplot_rsi
  • Determining bacterial ID:
    • New functions as.bactid and is.bactid to transform/ look up microbial ID's.
    • The existing function guess_bactid is now an alias of as.bactid
    • New Becker classification for Staphylococcus to categorise them into Coagulase Negative Staphylococci (CoNS) and Coagulase Positve Staphylococci (CoPS)
    • New Lancefield classification for Streptococcus to categorise them into Lancefield groups
  • For convience, new descriptive statistical functions kurtosis and skewness that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
  • Function g.test to perform the Χ2 distributed G-test, which use is the same as chisq.test
  • Function ratio to transform a vector of values to a preset ratio
    • For example: ratio(c(10, 500, 10), ratio = "1:2:1") would return 130, 260, 130
  • Support for Addins menu in RStudio to quickly insert %in% or %like% (and give them keyboard shortcuts), or to view the datasets that come with this package
  • Function p.symbol to transform p values to their related symbols: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  • Functions clipboard_import and clipboard_export as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the clipr package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)
  • New for frequency tables (function freq):
    • A vignette to explain its usage
    • Support for rsi (antimicrobial resistance) to use as input
    • Support for table to use as input: freq(table(x, y))
    • Support for existing functions hist and plot to use a frequency table as input: hist(freq(df$age))
    • Support for as.vector, as.data.frame, as_tibble and format
    • Support for quasiquotation: freq(mydata, mycolumn) is the same as mydata %>% freq(mycolumn)
    • Function top_freq function to return the top/below n items as vector
    • Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)
    • Possibility to globally set the default for the amount of items to print, with options(max.print.freq = n) where n is your preset value

Changed

  • Improvements for forecasting with resistance_predict and added more examples
  • More antibiotics added as parameters for EUCAST rules
  • Updated version of the septic_patients data set to better reflect the reality
  • Pretty printing for tibbles removed as it is not really the scope of this package
  • Printing of mic and rsi classes now returns all values - use freq to check distributions
  • Improved speed of key antibiotics comparison for determining first isolates
  • Column names for the key_antibiotics function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs
  • Speed improvement for the abname function
  • %like% now supports multiple patterns
  • Frequency tables are now actual data.frames with altered console printing to make it look like a frequency table. Because of this, the parameter toConsole is not longer needed.
  • Fix for freq where the class of an item would be lost
  • Small translational improvements to the septic_patients dataset and the column bactid now has the new class "bactid"
  • Small improvements to the microorganisms dataset (especially for Salmonella) and the column bactid now has the new class "bactid"
  • Combined MIC/RSI values will now be coerced by the rsi and mic functions:
    • as.rsi("<=0.002; S") will return S
    • as.mic("<=0.002; S") will return <=0.002
  • Now possible to coerce MIC values with a space between operator and value, i.e. as.mic("<= 0.002") now works
  • Classes rsi and mic do not add the attribute package.version anymore
  • Added "groups" option for atc_property(..., property). It will return a vector of the ATC hierarchy as defined by the WHO. The new function atc_groups is a convenient wrapper around this.
  • Build-in host check for atc_property as it requires the host set by url to be responsive
  • Improved first_isolate algorithm to exclude isolates where bacteria ID or genus is unavailable
  • Fix for warning hybrid evaluation forced for row_number (924b62) from the dplyr package v0.7.5 and above
  • Support for empty values and for 1 or 2 columns as input for guess_bactid (now called as.bactid)
    • So yourdata %>% select(genus, species) %>% as.bactid() now also works
  • Other small fixes

Other

0.2.0

Published on CRAN: 2018-05-03

New

  • Full support for Windows, Linux and macOS
  • Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
  • Function n_rsi to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise, see ?rsi
  • Function guess_bactid to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
  • Function guess_atc to determine the ATC of an antibiotic based on name, trade name, or known abbreviations
  • Function freq to create frequency tables, with additional info in a header
  • Function MDRO to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines.
  • New algorithm to determine weighted isolates, can now be "points" or "keyantibiotics", see ?first_isolate
  • New print format for tibbles and data.tables

Changed

  • Fixed rsi class for vectors that contain only invalid antimicrobial interpretations
  • Renamed dataset ablist to antibiotics
  • Renamed dataset bactlist to microorganisms
  • Added common abbreviations and trade names to the antibiotics dataset
  • Added more microorganisms to the microorganisms dataset
  • Added analysis examples on help page of dataset septic_patients
  • Added support for character vector in join functions
  • Added warnings when a join results in more rows after than before the join
  • Altered %like% to make it case insensitive
  • For parameters of functions first_isolate and EUCAST_rules column names are now case-insensitive
  • Functions as.rsi and as.mic now add the package name and version as attributes

Other

0.1.1

Published on CRAN: 2018-03-14

  • EUCAST_rules applies for amoxicillin even if ampicillin is missing
  • Edited column names to comply with GLIMS, the laboratory information system
  • Added more valid MIC values
  • Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
  • Added barplots for rsi and mic classes

0.1.0

Published on CRAN: 2018-02-22

  • First submission to CRAN.