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added mdr_tb()

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dr. M.S. (Matthijs) Berends
2019-05-23 16:58:59 +02:00
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commit 60983a1640
60 changed files with 1479 additions and 626 deletions
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NEWS.md
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# AMR 0.6.1.9001
# AMR 0.6.1.90xx
**Note: latest development version**
#### New
* Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
* Function `mo_name()` as alias of `mo_fullname()`
* Added guidelines of the WHO to determine mutli-drug resistance (MDR) for TB (`mdr_tb()`) and added a new vignette about MDR
#### Changed
* Completely reworked the `antibiotics` data set:
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* Column `ab` contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package
* Column `atc` contains the ATC code, used by WHO/WHOCC
* Column `cid` contains the CID code (Compound ID), used by PubChem
* Based on the Compound ID, more than a thousand official brand names have been added from many different countries
* Based on the Compound ID, almost 5,000 official brand names have been added from many different countries
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
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* Added ~5,000 more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function
* This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as 'increased exposure' and not 'intermediate' anymore. For functions like `portion_df()` and `count_df()` this means that their new parameter `combine_SI` is TRUE at default.
* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()`, `rsi()`
* Frequency tables of microbial IDs speed improvement
* Frequency tables (`freq()`):
* speed improvement for microbial IDs
* fixed level names in markdown
*
* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`
* Added ceftazidim intrinsic resistance to *Streptococci*
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+