AMR/NEWS.md

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2018-05-31 14:19:25 +02:00
# 0.2.0.90xx (development version)
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**Published on CRAN: (unpublished)**
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#### New
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* **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.
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* **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
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* Functions `as.bactid` and `is.bactid` to transform/look up microbial ID's; this replaces the function `guess_bactid` but it will remain available for backwards compatibility
2018-07-13 17:23:46 +02:00
* 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` 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`
* 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)
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* New for frequency tables (function `freq`):
* 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)`
* 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
2018-06-20 14:47:37 +02:00
#### Changed
2018-07-26 16:30:42 +02:00
* Improvements for forcasting with `resistance_predict` and added more examples
* More antibiotics for EUCAST rules
2018-07-30 01:18:40 +02:00
* Updated version of the `septic_patients` data set to better reflect the reality
2018-07-11 20:12:19 +02:00
* Pretty printing for tibbles removed as it is not really the scope of this package
2018-07-15 22:56:41 +02:00
* Improved speed of key antibiotics comparison for determining first isolates
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* 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
2018-07-15 22:56:41 +02:00
* Printing of class `mic` now shows all MIC values
* `%like%` now supports multiple patterns
2018-07-01 21:40:37 +02:00
* 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.
2018-07-23 14:14:03 +02:00
* 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](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
2018-06-19 10:05:38 +02:00
* 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
2018-07-23 14:14:03 +02:00
* 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
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* Other small fixes
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#### Other
* 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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**Published on CRAN: 2018-05-03**
#### 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
* 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
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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
#### 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`
* Renamed dataset `bactlist` to `microorganisms`
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* Added common abbreviations and trade names to the `antibiotics` dataset
* Added more microorganisms to the `microorganisms` dataset
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* 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
2018-04-25 15:33:58 +02:00
* 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
2018-04-25 15:33:58 +02:00
* Expanded `README.md` with more examples
* Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
2018-04-18 15:19:00 +02:00
* Added unit testing with the `testthat` package
* Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
2018-04-25 15:33:58 +02:00
* 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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**Published on CRAN: 2018-03-14**
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* `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
2018-04-18 15:19:00 +02:00
# 0.1.0
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**Published on CRAN: 2018-02-22**
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* First submission to CRAN.