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new class bactid

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dr. M.S. (Matthijs) Berends
2018-07-23 14:14:03 +02:00
parent 40de1b4ac2
commit 8421638b60
21 changed files with 408 additions and 251 deletions
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NEWS.md
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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:
* Gram-positive: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole, vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin
* Gram-negative: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole, gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem
* 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
* 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 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
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* Printing of class `mic` now shows all MIC values
* `%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*
* 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`
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* 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`
* 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
* Unit testing for R 3.0 and the latest available release: https://travis-ci.org/msberends/AMR