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dr. M.S. (Matthijs) Berends
2019-05-13 10:10:16 +02:00
parent 0444c4ed9d
commit 38a4421450
36 changed files with 475 additions and 213 deletions
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NEWS.md
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@ -6,7 +6,10 @@
#### Changed
* Completely reworked the `antibiotics` data set:
* All entries now have 3 different identifiers: a human readable EARS-Net code (`ab`, used by ECDC and WHONET), an ATC code (`atc`, used by WHO), and a CID code (`cid`, Compound ID, used by PubChem)
* All entries now have 3 different identifiers:
* 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
* 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
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Please create an issue in one of our repositories if you want additions in this file.
* Improved intelligence of looking up antibiotic tables in data set using `guess_ab_col()`
* 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
* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`.