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eucast rules fix, 1st isolate fix, website update

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dr. M.S. (Matthijs) Berends
2018-12-31 01:48:53 +01:00
parent 469b145d8c
commit 2e4d703338
51 changed files with 1473 additions and 1760 deletions
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35
NEWS.md
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@@ -2,15 +2,15 @@
**Note: this is the development version, which will eventually be released as AMR 0.6.0.**
#### New
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo` to identify an MO code.
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Support for [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* Function `mo_failures` to review values that could not be coerced to a valid MO code, using `as.mo`. This latter function will now only show a maximum of 25 uncoerced values.
* Function `mo_renamed` to get a list of all returned values from `as.mo` that have had taxonomic renaming
* Function `age` to calculate the (patients) age in years
* Function `age_groups` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.
* Functions `filter_first_isolate` and `filter_first_weighted_isolate()` to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
* Function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
* Function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
* Function `age()` to calculate the (patients) age in years
* Function `age_groups()` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.
* Functions `filter_first_isolate()` and `filter_first_weighted_isolate()` to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
```r
septic_patients %>% filter_first_isolate()
# or
@@ -25,7 +25,8 @@
```
#### Changed
* Improvements for `as.mo`:
* Fixed a critical bug in `eucast_rules()` where some rules that depend on previous applied rules would not be applied adequately
* Improvements for `as.mo()`:
* Finds better results when input is in other languages
* Better handling for subspecies
* Better handling for *Salmonellae*
@@ -33,18 +34,18 @@
* Manual now contains more info about the algorithms
* Progress bar will be shown when it takes more than 3 seconds to get results
* Support for formatted console text
* Function `first_isolate`:
* Function `first_isolate()`:
* Fixed a bug where distances between dates would not be calculated right - in the `septic_patients` data set this yielded a difference of 0.15% more isolates
* Will now use a column named like "patid" for the patient ID (parameter `col_patientid`), when this parameter was left blank
* Will now use a column named like "key(...)ab" or "key(...)antibiotics" for the key antibiotics (parameter `col_keyantibiotics`), when this parameter was left blank
* Will now use a column named like "key(...)ab" or "key(...)antibiotics" for the key antibiotics (parameter `col_keyantibiotics()`), when this parameter was left blank
* Removed parameter `output_logical`, the function will now always return a logical value
* Renamed parameter `filter_specimen` to `specimen_group`, although using `filter_specimen` will still work
* A note to the manual pages of the `portion` functions, that low counts can influence the outcome and that the `portion` functions may camouflage this, since they only return the portion (albeit being dependent on the `minimum` parameter)
* Function `mo_taxonomy` now contains the kingdom too
* Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank
* Reduce false positives for `is.rsi.eligible`
* Function `mo_taxonomy()` now contains the kingdom too
* Reduce false positives for `is.rsi.eligible()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
* Small text updates to summaries of class `rsi` and `mic`
* Frequency tables (`freq` function):
* Frequency tables (`freq()` function):
* Header info is now available as a list, with the `header` function
* Added header info for class `mo` to show unique count of families, genera and species
* Now honours the `decimal.mark` setting, which just like `format` defaults to `getOption("OutDec")`
@@ -52,10 +53,10 @@
* Fix for header text where all observations are `NA`
* New parameter `droplevels` to exclude empty factor levels when input is a factor
* Factor levels will be in header when present in input data
* Function `scale_y_percent` now contains the `limits` parameter
* Automatic parameter filling for `mdro`, `key_antibiotics` and `eucast_rules`
* Updated examples for resistance prediction (`resistance_predict` function)
* Fix for `as.mic` to support more values ending in (several) zeroes
* Function `scale_y_percent()` now contains the `limits` parameter
* Automatic parameter filling for `mdro()`, `key_antibiotics()` and `eucast_rules()`
* Updated examples for resistance prediction (`resistance_predict()` function)
* Fix for `as.mic()` to support more values ending in (several) zeroes
#### Other
* Updated licence text to emphasise GPL 2.0 and that this is an R package.