# 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 * Function `g.test` to perform the Χ2 distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test` * Function `ratio` to transform a vector of values to a preset ratio. For example: ```r 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` * 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 #### Changed * `%like%` now supports multiple patterns * Frequency tables are now actual `data.frame`s 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](https://www.whocc.no/atc/structure_and_principles/). 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`](https://github.com/tidyverse/dplyr/commit/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 #### Other * Unit testing for R 3.0 and the latest available release: https://travis-ci.org/msberends/AMR # 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. * Suggest your own via [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E) * [Exceptional resistances defined by EUCAST](http://www.eucast.org/expert_rules_and_intrinsic_resistance) 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 `tibble`s and `data.table`s #### 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](https://orcid.org) 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 * `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.