AMR/NEWS.md

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2018-08-22 00:02:26 +02:00
# 0.3.0.90xx (latest development version)
#### New
2018-09-24 23:33:29 +02:00
* The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
* Aliases for existing function `mo_property`
* Taxonomic names: `mo_phylum`, `mo_class`, `mo_order`, `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`
* Semantic names: `mo_fullname`, `mo_shortname`
* Microbial properties: `mo_type`, `mo_gramstain`.
They also come with support for German, Dutch, French, Italian, Spanish and Portuguese, and it defaults to the systems locale:
```r
mo_gramstain("E. coli")
# [1] "Gram negative"
mo_gramstain("E. coli", language = "de") # "de" = Deutsch / German
# [1] "Gramnegativ"
mo_gramstain("E. coli", language = "es") # "es" = Español / Spanish
# [1] "Gram negativo"
mo_fullname("S. group A") # when run on a on a Portuguese system
# [1] "Streptococcus grupo A"
```
Furthermore, old taxonomic names kan easily be looked up and give a note about the taxonomic change:
```r
mo_fullname("Pseudomonas facilis")
# Note: 'Pseudomonas facilis' was renamed to 'Acidovorax facilis' by Willems et al. in 1990
# [1] "Acidovorax facilis"
```
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* Functions `count_R`, `count_IR`, `count_I`, `count_SI` and `count_S` to selectively count resistant or susceptible isolates
* Extra function `count_df` (which works like `portion_df`) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables
2018-08-22 12:55:05 +02:00
* Function `is.rsi.eligible` to check for columns that have valid antimicrobial results, but do not have the `rsi` class yet. Transform the columns of your raw data with: `data %>% mutate_if(is.rsi.eligible, as.rsi)`
2018-09-14 10:31:21 +02:00
* Functions `as.mo` and `is.mo` as replacements for `as.bactid` and `is.bactid` (since the `microoganisms` data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The `as.mo` function determines microbial IDs using Artificial Intelligence (AI):
```r
as.mo("E. coli")
# [1] ESCCOL
as.mo("MRSA")
# [1] STAAUR
as.mo("S group A")
# [1] STCGRA
```
And with great speed too - on a quite regular Linux server from 2007 it takes us 0.009 seconds to transform 25,000 items:
```r
thousands_of_E_colis <- rep("E. coli", 25000)
microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s")
# Unit: seconds
# min median max neval
# 0.00861352 0.008774335 0.01952958 100
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```
2018-08-31 13:36:19 +02:00
* Renamed all previous references to `bactid` to `mo`, like:
* Column names inputs of `EUCAST_rules`, `first_isolate` and `key_antibiotics`
* Column names of datasets `microorganisms` and `septic_patients`
* All old syntaxes will still work with this version, but will throw warnings
2018-09-16 22:11:17 +02:00
* Function `labels_rsi_count` to print datalabels on a RSI `ggplot2` model
* Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`.
2018-09-24 23:33:29 +02:00
* Function `ab_property` and its aliases: `ab_name`, `ab_tradenames`, `ab_certe`, `ab_umcg` and `ab_trivial_nl`
* Introduction to AMR as a vignette
2018-08-22 00:02:26 +02:00
#### Changed
* Added almost 200 microorganisms to the `microorganisms` data set and removed the few viruses it contained
* Added three antimicrobial agents to the `antibiotics` data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
* Added 163 trade names to the `antibiotics` data set, it now contains 298 different trade names in total, e.g.:
```r
ab_official("Bactroban")
# [1] "Mupirocin"
ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"
ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"
```
* For `first_isolate`, rows will be ignored when there's no species available
2018-08-31 13:36:19 +02:00
* Function `ratio` is now deprecated and will be removed in a future release, as it is not really the scope of this package
* Fix for `as.mic` for values ending in zeroes after a real number
* Small fix where *B. fragilis* would not be found in the `microorganisms.umcg` data set
* Added `prevalence` column to the `microorganisms` data set
2018-08-22 00:02:26 +02:00
* Added parameters `minimum` and `as_percent` to `portion_df`
2018-08-23 01:01:50 +02:00
* Support for quasiquotation in the functions series `count_*` and `portions_*`, and `n_rsi`. This allows to check for more than 2 vectors or columns.
```r
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septic_patients %>% select(amox, cipr) %>% count_IR()
# which is the same as:
septic_patients %>% count_IR(amox, cipr)
septic_patients %>% portion_S(amcl)
septic_patients %>% portion_S(amcl, gent)
septic_patients %>% portion_S(amcl, gent, pita)
```
2018-08-22 00:02:26 +02:00
* Edited `ggplot_rsi` and `geom_rsi` so they can cope with `count_df`. The new `fun` parameter has value `portion_df` at default, but can be set to `count_df`.
2018-08-23 00:40:36 +02:00
* Fix for `ggplot_rsi` when the `ggplot2` package was not loaded
2018-09-16 22:11:17 +02:00
* Added datalabels function `labels_rsi_count` to `ggplot_rsi`
2018-08-23 21:27:15 +02:00
* Added possibility to set any parameter to `geom_rsi` (and `ggplot_rsi`) so you can set your own preferences
2018-09-03 10:04:49 +02:00
* Fix for joins, where predefined suffices would not be honoured
* Added parameter `quote` to the `freq` function
* Added longest en shortest character length in the frequency table (`freq`) header of class `character`
* Support for types (classes) list and matrix for `freq`
```r
my_matrix = with(septic_patients, matrix(c(age, sex), ncol = 2))
freq(my_matrix)
```
For lists, subsetting is possible:
```r
my_list = list(age = septic_patients$age, sex = septic_patients$sex)
my_list %>% freq(age)
my_list %>% freq(sex)
```
#### Other
* More unit tests to ensure better integrity of functions
2018-08-22 00:02:26 +02:00
# 0.3.0 (latest stable version)
2018-08-14 14:06:18 +02:00
**Published on CRAN: 2018-08-14**
2018-07-30 00:57:49 +02:00
2018-06-20 14:47:37 +02:00
#### New
2018-08-11 21:30:00 +02:00
* **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
2018-08-13 16:42:37 +02:00
* New function `portion_df` to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables
2018-07-17 19:51:09 +02:00
* **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
2018-08-11 21:30:00 +02:00
* Support for `ggplot2`
* New functions `geom_rsi`, `facet_rsi`, `scale_y_percent`, `scale_rsi_colours` and `theme_rsi`
* New wrapper function `ggplot_rsi` to apply all above functions on a data set:
* `septic_patients %>% select(tobr, gent) %>% ggplot_rsi` will show portions of S, I and R immediately in a pretty plot
2018-08-13 16:42:37 +02:00
* Support for grouped variables, see `?ggplot_rsi`
* Determining bacterial ID:
* New functions `as.bactid` and `is.bactid` to transform/ look up microbial ID's.
* The existing function `guess_bactid` is now an alias of `as.bactid`
* New Becker classification for *Staphylococcus* to categorise them into Coagulase Negative *Staphylococci* (CoNS) and Coagulase Positve *Staphylococci* (CoPS)
* New Lancefield classification for *Streptococcus* to categorise them into Lancefield groups
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
2018-07-17 19:51:09 +02:00
* 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`
2018-08-24 14:18:38 +02:00
* ~~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`~~
2018-07-17 19:51:09 +02:00
* 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)
2018-07-08 22:14:55 +02:00
* New for frequency tables (function `freq`):
* A vignette to explain its usage
2018-08-01 22:37:28 +02:00
* Support for `rsi` (antimicrobial resistance) to use as input
2018-07-09 14:02:58 +02:00
* Support for `table` to use as input: `freq(table(x, y))`
2018-07-08 22:14:55 +02:00
* Support for existing functions `hist` and `plot` to use a frequency table as input: `hist(freq(df$age))`
2018-07-16 16:41:48 +02:00
* Support for `as.vector`, `as.data.frame`, `as_tibble` and `format`
2018-07-08 22:14:55 +02:00
* 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
2018-08-13 11:00:53 +02:00
* Improvements for forecasting with `resistance_predict` and added more examples
* More antibiotics added as parameters 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
2018-08-01 22:37:28 +02:00
* Printing of `mic` and `rsi` classes now returns all values - use `freq` to check distributions
2018-07-15 22:56:41 +02:00
* Improved speed of key antibiotics comparison for determining first isolates
2018-07-19 15:11:23 +02:00
* 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
2018-08-13 11:00:53 +02:00
* Speed improvement for the `abname` function
* `%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
2018-07-28 10:48:27 +02:00
* Other small fixes
2018-05-09 11:44:46 +02:00
2018-07-10 12:27:07 +02:00
#### Other
2018-08-14 08:57:17 +02:00
* Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
* Linux and macOS: https://travis-ci.org/msberends/AMR
* Windows: https://ci.appveyor.com/project/msberends/amr
2018-08-03 09:59:39 +02:00
* Added thesis advisors to DESCRIPTION file
2018-07-10 12:27:07 +02:00
2018-08-14 14:06:18 +02:00
# 0.2.0
2018-07-30 00:57:49 +02:00
**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)
2018-05-02 14:56:25 +02:00
* Function `n_rsi` to count cases where antibiotic test results were available, to be used in conjunction with `dplyr::summarise`, see ?rsi
2018-04-25 15:33:58 +02:00
* 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
2018-04-18 15:19:00 +02:00
* New algorithm to determine weighted isolates, can now be `"points"` or `"keyantibiotics"`, see `?first_isolate`
2018-04-25 15:33:58 +02:00
* New print format for `tibble`s and `data.table`s
#### Changed
2018-05-02 14:56:25 +02:00
* Fixed `rsi` class for vectors that contain only invalid antimicrobial interpretations
2018-04-18 15:19:00 +02:00
* Renamed dataset `ablist` to `antibiotics`
* Renamed dataset `bactlist` to `microorganisms`
2018-04-25 15:33:58 +02:00
* Added common abbreviations and trade names to the `antibiotics` dataset
* Added more microorganisms to the `microorganisms` dataset
2018-04-18 15:19:00 +02:00
* 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)
2018-04-18 15:19:00 +02:00
# 0.1.1
2018-07-30 00:57:49 +02:00
**Published on CRAN: 2018-03-14**
2018-04-18 15:19:00 +02:00
* `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
2018-07-30 00:57:49 +02:00
**Published on CRAN: 2018-02-22**
2018-04-18 15:19:00 +02:00
* First submission to CRAN.