mirror of https://github.com/msberends/AMR.git
89 lines
6.7 KiB
Markdown
Executable File
89 lines
6.7 KiB
Markdown
Executable File
# 0.2.0.90xx (development version)
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#### New
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* **BREAKING**: `rsi_df` was removed in favour of new functions `resistance` and `susceptibility`. Now, all functions used to calculate resistance (`resistance` and `susceptibility`) or count isolates (`n_rsi`) use **hybrid evaluation**. This means calculations are not done in R directly but rather in C++ using the `Rcpp` package, making them 25 to 30 times faster. The function `rsi` still works, but is deprecated.
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* 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
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* 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
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* Function `g.test` as added to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
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* Function `ratio` was added to transform a vector of values to a preset ratio. For example:
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```r
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ratio(c(772, 1611, 737), ratio = "1:2:1")
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# [1] 780 1560 780
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```
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* Function `p.symbol` was added to transform p values to their related symbols: `0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1`
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* New for frequency tables (function `freq`):
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* A vignette to explain its usage
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* Support for `table` to use as input: `freq(table(x, y))`
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* Support for existing functions `hist` and `plot` to use a frequency table as input: `hist(freq(df$age))`
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* Support for `as.vector`, `as.data.frame`, `as_tibble` and `format`
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* Support for quasiquotation: `freq(mydata, mycolumn)` is the same as `mydata %>% freq(mycolumn)`
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* Function `top_freq` function to return the top/below *n* items as vector
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* Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)
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* 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
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* 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).
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#### Changed
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* Pretty printing for tibbles removed as it is not really the scope of this package
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* Improved speed of key antibiotics comparison for determining first isolates
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* Printing of class `mic` now shows all MIC values
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* `%like%` now supports multiple patterns
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* 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.
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* Small translational improvements to the `septic_patients` dataset
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* Small improvements to the `microorganisms` dataset, especially for *Salmonella*
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* Combined MIC/RSI values will now be coerced by the `rsi` and `mic` functions:
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* `as.rsi("<=0.002; S")` will return `S`
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* `as.mic("<=0.002; S")` will return `<=0.002`
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* Now possible to coerce MIC values with a space between operator and value, i.e. `as.mic("<= 0.002")` now works
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* 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.
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* Build-in host check for `atc_property` as it requires the host set by `url` to be responsive
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* Improved `first_isolate` algorithm to exclude isolates where bacteria ID or genus is unavailable
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* 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
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* Support for 1 or 2 columns as input for `guess_bactid`
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#### Other
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* Unit testing for R 3.0 and the latest available release: https://travis-ci.org/msberends/AMR
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# 0.2.0 (latest stable version)
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#### New
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* Full support for Windows, Linux and macOS
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* Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
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* Function `n_rsi` to count cases where antibiotic test results were available, to be used in conjunction with `dplyr::summarise`, see ?rsi
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* Function `guess_bactid` to **determine the ID** of a microorganism based on genus/species or known abbreviations like MRSA
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* Function `guess_atc` to **determine the ATC** of an antibiotic based on name, trade name, or known abbreviations
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* Function `freq` to create **frequency tables**, with additional info in a header
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* Function `MDRO` to **determine Multi Drug Resistant Organisms (MDRO)** with support for country-specific guidelines.
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* 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)
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* [Exceptional resistances defined by EUCAST](http://www.eucast.org/expert_rules_and_intrinsic_resistance) are also supported instead of countries alone
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* Functions `BRMO` and `MRGN` are wrappers for Dutch and German guidelines, respectively
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* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
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* New print format for `tibble`s and `data.table`s
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#### Changed
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* Fixed `rsi` class for vectors that contain only invalid antimicrobial interpretations
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* Renamed dataset `ablist` to `antibiotics`
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* Renamed dataset `bactlist` to `microorganisms`
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* Added common abbreviations and trade names to the `antibiotics` dataset
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* Added more microorganisms to the `microorganisms` dataset
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* Added analysis examples on help page of dataset `septic_patients`
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* Added support for character vector in `join` functions
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* Added warnings when a join results in more rows after than before the join
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* Altered `%like%` to make it case insensitive
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* For parameters of functions `first_isolate` and `EUCAST_rules` column names are now case-insensitive
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* Functions `as.rsi` and `as.mic` now add the package name and version as attributes
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#### Other
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* Expanded `README.md` with more examples
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* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
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* Added unit testing with the `testthat` package
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* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
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* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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# 0.1.1
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* `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
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* Edited column names to comply with GLIMS, the laboratory information system
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* Added more valid MIC values
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* Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
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* Added barplots for `rsi` and `mic` classes
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# 0.1.0
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* First submission to CRAN.
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