AMR/NEWS.md

0.2.0.90xx (development version)

Published on CRAN: (unpublished)

New

• BREAKING: rsi_df was removed in favour of new functions R, IR, SI and S to selectively calculate resistance or susceptibility. These functions use hybrid evaluation, which means that calculations are not done in R directly but rather in C++ using the Rcpp package, making them 20 to 30 times faster. The function rsi still works, but is deprecated.
• 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
• 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 forcasting with resistance_predict and added more examples
• More antibiotics 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
• %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

• Unit testing for all Linux and macOS releases of R 3.1 and higher: https://travis-ci.org/msberends/AMR

0.2.0 (latest stable version)

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.
  • Suggest your own via https://github.com/msberends/AMR/issues/new
  • Exceptional resistances defined by EUCAST are also supported instead of countries alone
  • Functions BRMO and MRGN are wrappers for Dutch and German guidelines, respectively
• 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

• Expanded README.md with more examples
• Added ORCID of authors to DESCRIPTION file
• Added unit testing with the testthat package
• Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
• Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)

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.