AMR/NEWS.md

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0.2.0.90xx (development version)

New

  • 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
  • For convience, 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
  • New for frequency tables (function freq):
    • A vignette to explain its usage
    • 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 and as_tibble
    • 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
  • Functions clipboard_import and clipboard_export as helper functions to quickly copy and paste from/to software like Excel and SPSS
  • Function g.test to perform the Χ2 distributed G-test
  • Function ratio to transform a vector of values to a preset ratio (convenient to use with g.test). For example:
ratio(c(772, 1611, 737), ratio = "1:2:1")
# [1]  780 1560  780
  • Function p.symbol to transform p value to their related symbol: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Changed

  • %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.
  • Small translational improvements to the septic_patients dataset
  • Small improvements to the microorganisms dataset, especially for Salmonella
  • 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
  • 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 1 or 2 columns as input for guess_bactid
  • Fix for printing tibbles where characters would be accidentally transformed to factors

0.2.0 (latest stable version)

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

  • 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

  • First submission to CRAN.