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dr. M.S. (Matthijs) Berends 18b75356a9 re-add atc_ddd and atc_groups

2019-01-27 13:33:43 +01:00

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AMR 0.5.0.90xx

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.
All ab_* functions are deprecated and replaced by atc_* functions:
```
ab_property -> atc_property()
ab_name -> atc_name()
ab_official -> atc_official()
ab_trivial_nl -> atc_trivial_nl()
ab_certe -> atc_certe()
ab_umcg -> atc_umcg()
ab_tradenames -> atc_tradenames()
```
These functions use as.atc() internally. The old atc_property has been renamed atc_online_property(). This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class atc or must be coerable to this class. Properties of these classes should start with the same class name, analogous to as.mo() and e.g. mo_genus.
New website: https://msberends.gitlab.io/AMR (built with the great pkgdown)
- Contains the complete manual of this package and all of its functions with an explanation of their parameters
- Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
New functions set_mo_source() and get_mo_source() to use your own predefined MO codes as input for as.mo() and consequently all mo_* functions
Support for the upcoming dplyr version 0.8.0
New function guess_ab_col() to find an antibiotic column in a table
New 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 10 uncoerced values and will refer to mo_failures().
New function mo_renamed() to get a list of all returned values from as.mo() that have had taxonomic renaming
New function age() to calculate the (patients) age in years
New 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.
New function ggplot_rsi_predict() as well as the base R plot() function can now be used for resistance prediction calculated with resistance_predict():
```
x <- resistance_predict(septic_patients, col_ab = "amox")
plot(x)
ggplot_rsi_predict(x)
```

Functions filter_first_isolate() and filter_first_weighted_isolate() to shorten and fasten filtering on data sets with antimicrobial results, e.g.:

septic_patients %>% filter_first_isolate(...)
# or
filter_first_isolate(septic_patients, ...)

is equal to:

septic_patients %>%
  mutate(only_firsts = first_isolate(septic_patients, ...)) %>%
  filter(only_firsts == TRUE) %>%
  select(-only_firsts)

New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the G-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR.

Changed

Added 65 antibiotics to the antibiotics data set, from the Pharmaceuticals Community Register of the European Commission
Removed columns atc_group1_nl and atc_group2_nl from the antibiotics data set
Functions atc_ddd() and atc_groups() have been renamed atc_online_ddd() and atc_online_groups(). The old function are deprecated and will be removed in a future version.
Function guess_mo() is now deprecated in favour of as.mo() and will be removed in future versions
Function guess_atc() is now deprecated in favour of as.atc() and will be removed in future versions
Function eucast_rules():
- Updated EUCAST Clinical breakpoints to version 9.0 of 1 January 2019
- Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately
- Emphasised in manual that penicillin is meant as benzylpenicillin (ATC J01CE01)
Improvements for as.mo():
- Fix for vector containing only empty values
- Finds better results when input is in other languages
- Better handling for subspecies
- Better handling for Salmonellae
- There will be looked for uncertain results at default - these results will be returned with an informative warning
- 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
- Console will return the percentage of uncoercable input
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
- 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)
Merged data sets microorganisms.certe and microorganisms.umcg into microorganisms.codes
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):
- 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")
- The new big.mark parameter will at default be "," when decimal.mark = "." and "." otherwise
- 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 (maximum of 5)
- Fix for using select() on frequency tables
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.

AMR 0.5.0

New

Repository moved to GitLab: https://gitlab.com/msberends/AMR
Function count_all to get all available isolates (that like all portion_* and count_* functions also supports summarise and group_by), the old n_rsi is now an alias of count_all
Function get_locale to determine language for language-dependent output for some mo_* functions. This is now the default value for their language parameter, by which the system language will be used at default.
Data sets microorganismsDT, microorganisms.prevDT, microorganisms.unprevDT and microorganisms.oldDT to improve the speed of as.mo. They are for reference only, since they are primarily for internal use of as.mo.
Function read.4D to read from the 4D database of the MMB department of the UMCG
Functions mo_authors and mo_year to get specific values about the scientific reference of a taxonomic entry

Changed

Functions MDRO, BRMO, MRGN and EUCAST_exceptional_phenotypes were renamed to mdro, brmo, mrgn and eucast_exceptional_phenotypes
EUCAST_rules was renamed to eucast_rules, the old function still exists as a deprecated function
Big changes to the eucast_rules function:
- Now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
- New parameter rules to specify which rules should be applied (expert rules, breakpoints, others or all)
- New parameter verbose which can be set to TRUE to get very specific messages about which columns and rows were affected
- Better error handling when rules cannot be applied (i.e. new values could not be inserted)
- The number of affected values will now only be measured once per row/column combination
- Data set septic_patients now reflects these changes
- Added parameter pipe for piperacillin (J01CA12), also to the mdro function
- Small fixes to EUCAST clinical breakpoint rules
Added column kingdom to the microorganisms data set, and function mo_kingdom to look up values
Tremendous speed improvement for as.mo (and subsequently all mo_* functions), as empty values wil be ignored a priori
Fewer than 3 characters as input for as.mo will return NA

Function as.mo (and all mo_* wrappers) now supports genus abbreviations with "species" attached

as.mo("E. species")        # B_ESCHR
mo_fullname("E. spp.")     # "Escherichia species"
as.mo("S. spp")            # B_STPHY
mo_fullname("S. species")  # "Staphylococcus species"

Added parameter combine_IR (TRUE/FALSE) to functions portion_df and count_df, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)
Fix for portion_*(..., as_percent = TRUE) when minimal number of isolates would not be met
Added parameter also_single_tested for portion_* and count_* functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see ?portion
Using portion_* functions now throws a warning when total available isolate is below parameter minimum
Functions as.mo, as.rsi, as.mic, as.atc and freq will not set package name as attribute anymore
Frequency tables - freq():
- Support for grouping variables, test with:
```
septic_patients %>% 
  group_by(hospital_id) %>% 
  freq(gender)
```
- Support for (un)selecting columns:
```
septic_patients %>% 
  freq(hospital_id) %>% 
  select(-count, -cum_count) # only get item, percent, cum_percent
```
- Check for hms::is.hms
- Now prints in markdown at default in non-interactive sessions
- No longer adds the factor level column and sorts factors on count again
- Support for class difftime
- New parameter na, to choose which character to print for empty values
- New parameter header to turn the header info off (default when markdown = TRUE)
- New parameter title to manually setbthe title of the frequency table
first_isolate now tries to find columns to use as input when parameters are left blank
Improvements for MDRO algorithm (function mdro)
Data set septic_patients is now a data.frame, not a tibble anymore
Removed diacritics from all authors (columns microorganisms$ref and microorganisms.old$ref) to comply with CRAN policy to only allow ASCII characters
Fix for mo_property not working properly
Fix for eucast_rules where some Streptococci would become ceftazidime R in EUCAST rule 4.5
Support for named vectors of class mo, useful for top_freq()
ggplot_rsi and scale_y_percent have breaks parameter
AI improvements for as.mo:
- "CRS" -> Stenotrophomonas maltophilia
- "CRSM" -> Stenotrophomonas maltophilia
- "MSSA" -> Staphylococcus aureus
- "MSSE" -> Staphylococcus epidermidis
Fix for join functions
Speed improvement for is.rsi.eligible, now 15-20 times faster
In g.test, when sum(x) is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
ab_name will try to fall back on as.atc when no results are found
Removed the addin to view data sets
Percentages will now will rounded more logically (e.g. in freq function)

Other

New dependency on package crayon, to support formatted text in the console
Dependency tidyr is now mandatory (went to Import field) since portion_df and count_df rely on it
Updated vignettes to comply with README

AMR 0.4.0

New

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.

New functions based on the 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
Author and year: mo_ref

They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:

mo_gramstain("E. coli")
# [1] "Gram negative"
mo_gramstain("E. coli", language = "de") # German
# [1] "Gramnegativ"
mo_gramstain("E. coli", language = "es") # Spanish
# [1] "Gram negativo"
mo_fullname("S. group A", language = "pt") # Portuguese
# [1] "Streptococcus grupo A"

Furthermore, former taxonomic names will give a note about the current taxonomic name:

mo_gramstain("Esc blattae")
# Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)
# [1] "Gram negative"

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
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)
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):
```
as.mo("E. coli")
# [1] B_ESCHR_COL
as.mo("MRSA")
# [1] B_STPHY_AUR
as.mo("S group A")
# [1] B_STRPTC_GRA
```
And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:
```
thousands_of_E_colis <- rep("E. coli", 25000)
microbenchmark::microbenchmark(as.mo(thousands_of_E_colis), unit = "s")
# Unit: seconds
#         min       median         max  neval
#  0.01817717  0.01843957  0.03878077    100
```
Added parameter reference_df for as.mo, so users can supply their own microbial IDs, name or codes as a reference table
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
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.
Function ab_property and its aliases: ab_name, ab_tradenames, ab_certe, ab_umcg and ab_trivial_nl
Introduction to AMR as a vignette
Removed clipboard functions as it violated the CRAN policy
Renamed septic_patients$sex to septic_patients$gender

Changed

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.:

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
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
Added parameters minimum and as_percent to portion_df

Support for quasiquotation in the functions series count_* and portions_*, and n_rsi. This allows to check for more than 2 vectors or columns.

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)

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.
Fix for ggplot_rsi when the ggplot2 package was not loaded
Added datalabels function labels_rsi_count to ggplot_rsi
Added possibility to set any parameter to geom_rsi (and ggplot_rsi) so you can set your own preferences
Fix for joins, where predefined suffices would not be honoured
Added parameter quote to the freq function
Added generic function diff for frequency tables
Added longest en shortest character length in the frequency table (freq) header of class character

Support for types (classes) list and matrix for freq

my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2))
freq(my_matrix)

For lists, subsetting is possible:

my_list = list(age = septic_patients$age, gender = septic_patients$gender)
my_list %>% freq(age)
my_list %>% freq(gender)

Other

More unit tests to ensure better integrity of functions

AMR 0.3.0

New

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.
- 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
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
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
  - 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
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 Χ² distributed G-test, which use is the same as chisq.test
~~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~~
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)
New for frequency tables (function freq):
- A vignette to explain its usage
- Support for rsi (antimicrobial resistance) to use as input
- Support for table to use as input: freq(table(x, y))
- Support for existing functions hist and plot to use a frequency table as input: hist(freq(df$age))
- Support for as.vector, as.data.frame, as_tibble and format
- 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

Changed

Improvements for forecasting with resistance_predict and added more examples
More antibiotics added as parameters for EUCAST rules
Updated version of the septic_patients data set to better reflect the reality
Pretty printing for tibbles removed as it is not really the scope of this package
Printing of mic and rsi classes now returns all values - use freq to check distributions
Improved speed of key antibiotics comparison for determining first isolates
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
Speed improvement for the abname function
%like% now supports multiple patterns
Frequency tables are now actual data.frames with altered console printing to make it look like a frequency table. Because of this, the parameter toConsole is not longer needed.
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. 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
Improved first_isolate algorithm to exclude isolates where bacteria ID or genus is unavailable
Fix for warning hybrid evaluation forced for row_number (924b62) from the dplyr package v0.7.5 and above
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 small fixes

Other

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
Added thesis advisors to DESCRIPTION file

AMR 0.2.0

New

Full support for Windows, Linux and macOS
Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)
Function n_rsi to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise, see ?rsi
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.
- Exceptional resistances defined by EUCAST are also supported instead of countries alone
- Functions BRMO and MRGN are wrappers for Dutch and German guidelines, respectively
New algorithm to determine weighted isolates, can now be "points" or "keyantibiotics", see ?first_isolate
New print format for tibbles and data.tables

Changed

Fixed rsi class for vectors that contain only invalid antimicrobial interpretations
Renamed dataset ablist to antibiotics
Renamed dataset bactlist to microorganisms
Added common abbreviations and trade names to the antibiotics dataset
Added more microorganisms to the microorganisms dataset
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
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

Expanded README.md with more examples
Added ORCID of authors to DESCRIPTION file
Added unit testing with the testthat package
Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)

AMR 0.1.1

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

AMR 0.1.0

First submission to CRAN.

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AMR 0.5.0.90xx

New

Changed

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AMR 0.5.0

New

Changed

Other

AMR 0.4.0

New

Changed

Other

AMR 0.3.0

New

Changed

Other

AMR 0.2.0

New

Changed

Other

AMR 0.1.1

AMR 0.1.0

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