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Executable File
AMR
1.6.0.9056
Last updated: 21 May 2021
Breaking change
- All antibiotic class selectors (such as
carbapenems()
,aminoglycosides()
) can now be used for filtering as well, making all their accompanyingfilter_*()
functions redundant (such asfilter_carbapenems()
,filter_aminoglycosides()
). These functions are now deprecated and will be removed in a next release.# select columns with results for carbapenems example_isolates[, carbapenems()] # base R example_isolates %>% select(carbapenems()) # dplyr # filter rows for resistance in any carbapenem example_isolates[any(carbapenems() == "R"), ] # base R example_isolates %>% filter(any(carbapenems() == "R")) # dplyr example_isolates %>% filter(if_any(carbapenems(), ~.x == "R")) # dplyr (formal) # filter rows for resistance in all carbapenems example_isolates[all(carbapenems() == "R"), ] # base R example_isolates[carbapenems() == "R", ] example_isolates %>% filter(all(carbapenems() == "R")) # dplyr example_isolates %>% filter(carbapenems() == "R")
New
- Function
custom_eucast_rules()
that brings support for custom AMR rules ineucast_rules()
- Function
italicise_taxonomy()
to make taxonomic names within a string italic, with support for markdown and ANSI - Support for all four methods to determine first isolates as summarised by Hindler et al. (doi: 10.1086/511864): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
- The
first_isolate()
function gained the argumentmethod
that has to be "phenotype-based", "episode-based", "patient-based", or "isolate-based". The old behaviour is equal to "episode-based". The new default is "phenotype-based" if antimicrobial test results are available, and "episode-based" otherwise. This new default will yield slightly more isolates for selection (which is a good thing). - Since fungal isolates can also be selected, the functions
key_antibiotics()
andkey_antibiotics_equal()
are now deprecated in favour of thekey_antimicrobials()
andantimicrobials_equal()
functions. Also, the newall_antimicrobials()
function works like the oldkey_antibiotics()
function, but includes any column with antimicrobial test results. Usingkey_antimicrobials()
still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a newantifungal
argument to set antifungal agents (antimycotics). - Using
type == "points"
in thefirst_isolate()
function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the newall_antimicrobials()
- The
first_isolate()
function can now take a vector of values forcol_keyantibiotics
and can have an episode length ofInf
- Since the phenotype-based method is the new default,
filter_first_isolate()
renders thefilter_first_weighted_isolate()
function redundant. For this reason,filter_first_weighted_isolate()
is now deprecated. - The documentation of the
first_isolate()
andkey_antimicrobials()
functions has been completely rewritten.
- The
- Function
betalactams()
as additional antbiotic column selector and functionfilter_betalactams()
as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins. - A
ggplot()
method forresistance_predict()
Changed
- Custom MDRO guidelines (
mdro()
,custom_mdro_guideline()
):- Custom MDRO guidelines can now be combined with other custom MDRO guidelines using
c()
- Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule
- Custom MDRO guidelines can now be combined with other custom MDRO guidelines using
- Fix for
age_groups()
for persons aged zero - The
example_isolates
data set now contains some (fictitious) zero-year old patients - Fix for minor translation errors
- Printing of microbial codes in a
data.frame
ortibble
now gives a warning if the data contains old microbial codes (from a previous AMR package version) - Extended the
like()
functions:- Now checks if
pattern
is a valid regular expression - Added
%unlike%
and%unlike_case%
(as negations of the existing%like%
and%like_case%
). This greatly improves readability:if (!grepl("EUCAST", guideline)) ... # same: if (guideline %unlike% "EUCAST") ...
- Altered the RStudio addin, so it now iterates over
%like%
->%unlike%
->%like_case%
->%unlike_case%
if you keep pressing your keyboard shortcut
- Now checks if
- Fixed an installation error on R-3.0
- Added
info
argument toas.mo()
to turn on/off the progress bar - Fixed a bug where
col_mo
in some functions (esp.eucast_rules()
andmdro()
) could not be a column name of themicroorganisms
data set as it would throw an error - Fix for transforming numeric values to RSI (
as.rsi()
) when thevctrs
package is loaded (i.e., when using tidyverse) - Colour fix for using
barplot()
on an RSI class - Added 25 common system codes for bacteria to the
microorganisms.codes
data set - Added 16 common system codes for antimicrobial agents to the
antibiotics
data set - Fix for using
skimr::skim()
on classesmo
,mic
anddisk
when using the just releaseddplyr
v1.0.6 - Updated
skimr::skim()
usage for MIC values to also include 25th and 75th percentiles - Fix for plotting missing MIC/disk diffusion values
- Updated join functions to always use
dplyr
join functions if thedplyr
package is installed - now also preserving grouped variables - Antibiotic class selectors (such as
cephalosporins()
) now maintain the column order from the original data - Fix for selecting columns using
fluoroquinolones()
Other
- All unit tests are now processed by the
tinytest
package, instead of thetestthat
package. Thetestthat
package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, thetinytest
package is very lightweight and dependency-free.
AMR
1.6.0
New
- Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the
eucast_rules()
function and inas.rsi()
to interpret MIC and disk diffusion values. This is now the default guideline in this package.- Added function
eucast_dosage()
to get adata.frame
with advised dosages of a certain bug-drug combination, which is based on the newdosage
data set - Added data set
dosage
to fuel the neweucast_dosage()
function and to make this data available in a structured way - Existing data set
example_isolates
now reflects the latest EUCAST rules
- Added function
- Added argument
only_rsi_columns
for some functions, which defaults toFALSE
, to indicate if the functions must only be applied to columns that are of class<rsi>
(i.e., transformed withas.rsi()
). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:- All antibiotic selector functions (
ab_class()
and its wrappers, such asaminoglycosides()
,carbapenems()
,penicillins()
) - All antibiotic filter functions (
filter_ab_class()
and its wrappers, such asfilter_aminoglycosides()
,filter_carbapenems()
,filter_penicillins()
) eucast_rules()
mdro()
(including wrappers such asbrmo()
,mrgn()
andeucast_exceptional_phenotypes()
)guess_ab_col()
- All antibiotic selector functions (
- Functions
oxazolidinones()
(an antibiotic selector function) andfilter_oxazolidinones()
(an antibiotic filter function) to select/filter on e.g. linezolid and tedizolidlibrary(dplyr) x <- example_isolates %>% select(date, hospital_id, oxazolidinones()) #> Selecting oxazolidinones: column 'LNZ' (linezolid) x <- example_isolates %>% filter_oxazolidinones() #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"
- Support for custom MDRO guidelines, using the new
custom_mdro_guideline()
function, please seemdro()
for additional info ggplot()
generics for classes<mic>
and<disk>
- Function
mo_is_yeast()
, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
Themo_kingdom(c("Aspergillus", "Candida")) #> [1] "Fungi" "Fungi" mo_is_yeast(c("Aspergillus", "Candida")) #> [1] FALSE TRUE # usage for filtering data: example_isolates[which(mo_is_yeast()), ] # base R example_isolates %>% filter(mo_is_yeast()) # dplyr
mo_type()
function has also been updated to reflect this change:mo_type(c("Aspergillus", "Candida")) # [1] "Fungi" "Yeasts" mo_type(c("Aspergillus", "Candida"), language = "es") # also supported: de, nl, fr, it, pt #> [1] "Hongos" "Levaduras"
- Added Pretomanid (PMD, J04AK08) to the
antibiotics
data set - MIC values (see
as.mic()
) can now be used in any mathematical processing, such as usage inside functionsmin()
,max()
,range()
, and with binary operators (+
,-
, etc.). This allows for easy distribution analysis and fast filtering on MIC values:x <- random_mic(10) x #> Class <mic> #> [1] 128 0.5 2 0.125 64 0.25 >=256 8 16 4 x[x > 4] #> Class <mic> #> [1] 128 64 >=256 8 16 range(x) #> [1] 0.125 256.000 range(log2(x)) #> [1] -3 8
Changed
- Updated the bacterial taxonomy to 3 March 2021 (using LPSN)
- Added 3,372 new species and 1,523 existing species became synomyms
- The URL of a bacterial species (
mo_url()
) will now lead to https://lpsn.dsmz.de
- Big update for plotting classes
rsi
,<mic>
, and<disk>
:- Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
- All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
- Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see
translate
) - Plotting is now possible with base R using
plot()
and with ggplot2 usingggplot()
on any vector of MIC and disk diffusion values
- Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the
microorganisms
data set is.rsi()
andis.rsi.eligible()
now return a vector ofTRUE
/FALSE
when the input is a data set, by iterating over all columns- Using functions without setting a data set (e.g.,
mo_is_gram_negative()
,mo_is_gram_positive()
,mo_is_intrinsic_resistant()
,first_isolate()
,mdro()
) now work withdplyr
sgroup_by()
again first_isolate()
can be used withgroup_by()
(also when using a dot.
as input for the data) and now returns the names of the groups- Updated the data set
microorganisms.codes
(which contains popular LIS and WHONET codes for microorganisms) for some species of Mycobacterium that previously incorrectly returned M. africanum - WHONET code
"PNV"
will now correctly be interpreted asPHN
, the antibiotic code for phenoxymethylpenicillin ('peni V') - Fix for verbose output of
mdro(..., verbose = TRUE)
for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only P. aeruginosa) is.rsi.eligible()
now detects if the column name resembles an antibiotic name or code and now returnsTRUE
immediately if the input contains any of the values "R", "S" or "I". This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.- Functions
get_episode()
andis_new_episode()
now support less than a day as value for argumentepisode_days
(e.g., to include one patient/test per hour) - Argument
ampc_cephalosporin_resistance
ineucast_rules()
now also applies to value "I" (not only "S") - Functions
print()
andsummary()
on a Principal Components Analysis object (pca()
) now print additional group info if the original data was grouped usingdplyr::group_by()
- Improved speed and reliability of
guess_ab_col()
. As this also internally improves the reliability offirst_isolate()
andmdro()
, this might have a slight impact on the results of those functions. - Fix for
mo_name()
when used in other languages than English - The
like()
function (and its fast alias%like%
) now always use Perl compatibility, improving speed for many functions in this package (e.g.,as.mo()
is now up to 4 times faster) - Staphylococcus cornubiensis is now correctly categorised as coagulase-positive
random_disk()
andrandom_mic()
now have an expanded range in their randomisation- Support for GISA (glycopeptide-intermediate S. aureus), so e.g.
mo_genus("GISA")
will return"Staphylococcus"
- Added translations of German and Spanish for more than 200 antimicrobial drugs
- Speed improvement for
as.ab()
when the input is an official name or ATC code - Added argument
include_untested_rsi
to thefirst_isolate()
functions (defaults toTRUE
to keep existing behaviour), to be able to exclude rows where all R/SI values (class<rsi>
, seeas.rsi()
) are empty
Other
- Big documentation updates
- Loading the package (i.e.,
library(AMR)
) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
AMR
1.5.0
New
- Functions
get_episode()
andis_new_episode()
to determine (patient) episodes which are not necessarily based on microorganisms. Theget_episode()
function returns the index number of the episode per group, while theis_new_episode()
function returns valuesTRUE
/FALSE
to indicate whether an item in a vector is the start of a new episode. They also supportdplyr
s grouping (i.e. usinggroup_by()
):library(dplyr) example_isolates %>% group_by(patient_id, hospital_id) %>% filter(is_new_episode(date, episode_days = 60))
- Functions
mo_is_gram_negative()
andmo_is_gram_positive()
as wrappers aroundmo_gramstain()
. They always returnTRUE
orFALSE
(except when the input isNA
or the MO code isUNKNOWN
), thus always returnFALSE
for species outside the taxonomic kingdom of Bacteria. - Function
mo_is_intrinsic_resistant()
to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020. - Functions
random_mic()
,random_disk()
andrandom_rsi()
for random value generation. The functionsrandom_mic()
andrandom_disk()
take microorganism names and antibiotic names as input to make generation more realistic.
Changed
-
New argument
ampc_cephalosporin_resistance
ineucast_rules()
to correct for AmpC de-repressed cephalosporin-resistant mutants -
Interpretation of antimicrobial resistance -
as.rsi()
:- Reference data used for
as.rsi()
can now be set by the user, using thereference_data
argument. This allows for using own interpretation guidelines. The user-set data must have the same structure asrsi_translation
. - Better determination of disk zones and MIC values when running
as.rsi()
on a data.frame - Fix for using
as.rsi()
on a data.frame in older R versions as.rsi()
on a data.frame will not print a message anymore if the values are already clean R/SI values- If using
as.rsi()
on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this - Fix for using
as.rsi()
on adata.frame
that only contains one column for antibiotic interpretations
- Reference data used for
-
Some functions are now context-aware when used inside
dplyr
verbs, such asfilter()
,mutate()
andsummarise()
. This means that then the data argument does not need to be set anymore. This is the case for the new functions:mo_is_gram_negative()
mo_is_gram_positive()
mo_is_intrinsic_resistant()
... and for the existing functions:
first_isolate()
,key_antibiotics()
,mdro()
,brmo()
,mrgn()
,mdr_tb()
,mdr_cmi2012()
,eucast_exceptional_phenotypes()
# to select first isolates that are Gram-negative # and view results of cephalosporins and aminoglycosides: library(dplyr) example_isolates %>% filter(first_isolate(), mo_is_gram_negative()) %>% select(mo, cephalosporins(), aminoglycosides()) %>% as_tibble()
-
For antibiotic selection functions (such as
cephalosporins()
,aminoglycosides()
) to select columns based on a certain antibiotic group, the dependency on thetidyselect
package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):# above example in base R: example_isolates[which(first_isolate() & mo_is_gram_negative()), c("mo", cephalosporins(), aminoglycosides())]
-
For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the
typed
package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined. -
Fix for
set_mo_source()
, that previously would not remember the file location of the original file -
Deprecated function
p_symbol()
that not really fits the scope of this package. It will be removed in a future version. See here for the source code to preserve it. -
Updated coagulase-negative staphylococci determination with Becker et al. 2020 (PMID 32056452), meaning that the species S. argensis, S. caeli, S. debuckii, S. edaphicus and S. pseudoxylosus are now all considered CoNS
-
Fix for using argument
reference_df
inas.mo()
andmo_*()
functions that contain old microbial codes (from previous package versions) -
Fixed a bug where
mo_uncertainties()
would not return the results based on the MO matching score -
Fixed a bug where
as.mo()
would not return results for known laboratory codes for microorganisms -
Fixed a bug where
as.ab()
would sometimes fail -
Better tibble printing for MIC values
-
Fix for plotting MIC values with
plot()
-
Added
plot()
generic to class<disk>
-
LA-MRSA and CA-MRSA are now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g.
mo_genus("LA-MRSA")
will return"Staphylococcus"
andmo_is_gram_positive("LA-MRSA")
will returnTRUE
. -
Fix for printing class in tibbles when all values are
NA
-
Fix for
mo_shortname()
when the input containsNA
-
If
as.mo()
takes more than 30 seconds, some suggestions will be done to improve speed
Other
- All messages and warnings thrown by this package now break sentences on whole words
- More extensive unit tests
- Internal calls to
options()
were all removed in favour of a new internal environmentpkg_env
- Improved internal type setting (among other things: replaced all
sapply()
calls withvapply()
) - Added CodeFactor as a continuous code review to this package: https://www.codefactor.io/repository/github/msberends/amr/
- Added Dr. Rogier Schade as contributor
AMR
1.4.0
New
-
Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the
eucast_rules()
function can now correct for more than 180 different antibiotics and themdro()
function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. Theeucast_rules()
function consequently gained the argumentsversion_breakpoints
(at the moment defaults to v10.0, 2020) andversion_expertrules
(at the moment defaults to v3.2, 2020). Theexample_isolates
data set now also reflects the change from v3.1 to v3.2. Themdro()
function now acceptsguideline == "EUCAST3.1"
andguideline == "EUCAST3.2"
. -
A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
-
Data set
intrinsic_resistant
. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns:microorganism
andantibiotic
.Curious about which enterococci are actually intrinsic resistant to vancomycin?
library(AMR) library(dplyr) intrinsic_resistant %>% filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% pull(microorganism) #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
-
Support for veterinary ATC codes
-
Support for skimming classes
<rsi>
,<mic>
,<disk>
and<mo>
with theskimr
package
Changed
- Although advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.
- Improvements for
as.rsi()
:- Support for using
dplyr
'sacross()
to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.# until dplyr 1.0.0 your_data %>% mutate_if(is.mic, as.rsi) your_data %>% mutate_if(is.disk, as.rsi) # since dplyr 1.0.0 your_data %>% mutate(across(where(is.mic), as.rsi)) your_data %>% mutate(across(where(is.disk), as.rsi))
- Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g.
as.rsi(df, col1:col9)
- Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.
- Added argument 'add_intrinsic_resistance' (defaults to
FALSE
), that considers intrinsic resistance according to EUCAST - Fixed a bug where in EUCAST rules the breakpoint for R would be interpreted as ">=" while this should have been "<"
- Support for using
- Added intelligent data cleaning to
as.disk()
, so numbers can also be extracted from text and decimal numbers will always be rounded up:as.disk(c("disk zone: 23.4 mm", 23.4)) #> Class <disk> #> [1] 24 24
- Improvements for
as.mo()
:- A completely new matching score for ambiguous user input, using
mo_matching_score()
. Any user input value that could mean more than one taxonomic entry is now considered 'uncertain'. Instead of a warning, a message will be thrown and the accompanyingmo_uncertainties()
has been changed completely; it now prints all possible candidates with their matching score. - Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using
mo_*
functions likemo_name()
on microoganism IDs. - Added argument
ignore_pattern
toas.mo()
which can also be given tomo_*
functions likemo_name()
, to exclude known non-relevant input from analysing. This can also be set with the optionAMR_ignore_pattern
.
- A completely new matching score for ambiguous user input, using
get_locale()
now uses at defaultSys.getenv("LANG")
or, ifLANG
is not set,Sys.getlocale()
. This can be overwritten by setting the optionAMR_locale
.- Big speed improvement for
eucast_rules()
- Overall speed improvement by tweaking joining functions
- Function
mo_shortname()
now returns the genus for input where the species is unknown - BORSA is now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g.
mo_genus("BORSA")
will return "Staphylococcus" - Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies:
tibble
printing support for classes<rsi>
,<mic>
,<disk>
,<ab>
and<mo>
. When usingtibble
s containing antimicrobial columns (class<rsi>
), "S" will print in green, "I" will print in yellow and "R" will print in red. Microbial IDs (class<mo>
) will emphasise on the genus and species, not on the kingdom. - Names of antiviral agents in data set
antivirals
now have a starting capital letter, like it is the case in theantibiotics
data set - Updated the documentation of the
WHONET
data set to clarify that all patient names are fictitious - Small
as.ab()
algorithm improvements - Fix for combining MIC values with raw numbers, i.e.
c(as.mic(2), 2)
previously failed but now returns a valid MIC class ggplot_rsi()
andgeom_rsi()
gained argumentsminimum
andlanguage
, to influence the internal use ofrsi_df()
- Changes in the
antibiotics
data set:- Updated oral and parental DDDs from the WHOCC
- Added abbreviation "piptazo" to 'Piperacillin/tazobactam' (TZP)
- 'Penicillin G' (for intravenous use) is now named 'Benzylpenicillin' (code
PEN
) - 'Penicillin V' (for oral use, code
PNV
) was removed, since its actual entry 'Phenoxymethylpenicillin' (codePHN
) already existed - The group name (
antibiotics$group
) of 'Linezolid' (LNZ
), 'Cycloserine' (CYC
), 'Tedizolid' (TZD
) and 'Thiacetazone' (THA
) is now "Oxazolidinones" instead of "Other antibacterials"
- Added support for using
unique()
on classes<rsi>
,<mic>
,<disk>
,<ab>
and<mo>
- Added argument
excess
to thekurtosis()
function (defaults toFALSE
), to return the excess kurtosis, defined as the kurtosis minus three.
Other
- Removed functions
portion_R()
,portion_S()
andportion_I()
that were deprecated since version 0.9.0 (November 2019) and were replaced withproportion_R()
,proportion_S()
andproportion_I()
- Removed unnecessary references to the
base
package - Added packages that could be useful for some functions to the
Suggests
field of theDESCRIPTION
file
AMR
1.3.0
New
- Function
ab_from_text()
to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it usesas.ab()
internally - Tidyverse selection helpers for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like
dplyr::select()
andtidyr::pivot_longer()
:library(dplyr) # Columns 'IPM' and 'MEM' are in the example_isolates data set example_isolates %>% select(carbapenems()) #> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
- Added
mo_domain()
as an alias tomo_kingdom()
- Added function
filter_penicillins()
to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup Beta-lactam antibacterials, penicillins) - Added official antimicrobial names to all
filter_ab_class()
functions, such asfilter_aminoglycosides()
- Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the
antibiotics
data set - Added Monuril as trade name for fosfomycin
- Added argument
conserve_capped_values
toas.rsi()
for interpreting MIC values - it makes sure that values starting with "<" (but not "<=") will always return "S" and values starting with ">" (but not ">=") will always return "R". The default behaviour ofas.rsi()
has not changed, so you need to specifically doas.rsi(..., conserve_capped_values = TRUE)
.
Changed
-
Big speed improvement for using any function on microorganism codes from earlier package versions (prior to
AMR
v1.2.0), such asas.mo()
,mo_name()
,first_isolate()
,eucast_rules()
,mdro()
, etc.As a consequence, very old microbial codes (from
AMR
v0.5.0 and lower) are not supported anymore. Useas.mo()
on your microorganism names or codes to transform them to current abbreviations used in this package. -
Improvements for
susceptibility()
andresistance()
and allcount_*()
,proportion_*()
functions:- 95% speed improvement by using other base R functions for calculation
- Using unexisting columns wil now return an error instead of dropping them silently
- Using variables for column names (as well as selectors like
dplyr::all_of()
) now works again
-
Improvements for
as.ab()
:- Dramatic improvement of the algorithm behind
as.ab()
, making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more - Added progress bar
- Fixed a bug where
as.ab()
would return an error on invalid input values - The
as.ab()
function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
- Dramatic improvement of the algorithm behind
-
Fixed a bug where
eucast_rules()
would not work on a tibble when thetibble
ordplyr
package was loaded -
Fixed a bug for CLSI 2019 guidelines (using
as.rsi()
), that also included results for animals. It now only contains interpretation guidelines for humans. -
All
*_join_microorganisms()
functions andbug_drug_combinations()
now return the original data class (e.g.tibble
s anddata.table
s) -
For functions
rsi_df()
,proportion_df()
andcount_df()
:- Fixed a bug for using grouped versions
- Fixed a bug where not all different antimicrobial results were added as rows
- Fixed a bug when only calculating counts (
count_df()
) when all antibiotics in the data set have onlyNA
s
-
Improved auto-determination for columns of types
<mo>
and<Date>
-
Fixed a bug in
bug_drug_combinations()
for when only one antibiotic was in the input data -
Changed the summary for class
<rsi>
, to highlight the %SI vs. %R -
Improved error handling, giving more useful info when functions return an error
-
Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
-
Speed improvement for
mdro()
andfilter_ab_class()
-
New option
arrows_textangled
forggplot_pca()
to indicate whether the text at the end of the arrows should be angled (defaults toTRUE
, as it was in previous versions) -
Added parenteral DDD to benzylpenicillin
-
Fixed a bug where
as.mic()
could not handle dots without a leading zero (like"<=.25
)
Other
- Moved primary location of this project from GitLab to GitHub, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
AMR
1.2.0
Breaking
-
Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
Making this package independent of especially the tidyverse (e.g. packages
dplyr
andtidyr
) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.Negative effects of this change are:
- Function
freq()
that was borrowed from thecleaner
package was removed. Usecleaner::freq()
, or runlibrary("cleaner")
before you usefreq()
. Printing values of classmo
orrsi
in a tibble will no longer be in colour and printingrsi
in a tibble will show the class<ord>
, not<rsi>
anymore. This is purely a visual effect.All functions from themo_*
family (likemo_name()
andmo_gramstain()
) are noticeably slower when running on hundreds of thousands of rows.- For developers: classes
mo
andab
now both also inherit classcharacter
, to support any data transformation. This change invalidates code that checks for class length == 1.
- Function
Changed
- Taxonomy:
- Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using
first_isolate()
), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour. - Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string)
- Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using
- EUCAST rules:
-
The
eucast_rules()
function no longer applies "other" rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value forrules
is nowc("breakpoints", "expert")
instead of"all"
, but this can be changed by the user. To return to the old behaviour, setoptions(AMR.eucast_rules = "all")
. -
Fixed a bug where checking antimicrobial results in the original data were not regarded as valid R/SI values
-
All "other" rules now apply for all drug combinations in the
antibiotics
data set these two rules:- A drug with enzyme inhibitor will be set to S if the drug without enzyme inhibitor is S
- A drug without enzyme inhibitor will be set to R if the drug with enzyme inhibitor is R
This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/avibactam, trimethoprim/sulfamethoxazole, etc.
-
Added official drug names to verbose output of
eucast_rules()
-
- Added function
ab_url()
to return the direct URL of an antimicrobial agent from the official WHO website - Improvements for algorithm in
as.ab()
, so that e.g.as.ab("ampi sul")
andab_name("ampi sul")
work - Functions
ab_atc()
andab_group()
now returnNA
if no antimicrobial agent could be found - Small fix for some text input that could not be coerced as valid MIC values
- Fix for interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood)
- Fix for
set_mo_source()
to make sure that columnmo
will always be the second column - Added abbreviation "cfsc" for Cefoxitin and "cfav" for Ceftazidime/avibactam
Other
- Removed previously deprecated function
p.symbol()
- it was replaced withp_symbol()
- Removed function
read.4d()
, that was only useful for reading data from an old test database.
AMR
1.1.0
New
- Support for easy principal component analysis for AMR, using the new
pca()
function - Plotting biplots for principal component analysis using the new
ggplot_pca()
function
Changed
- Improvements for the algorithm used by
as.mo()
(and consequently allmo_*
functions, that useas.mo()
internally):- Support for codes ending with
SPE
for species, like"ESCSPE"
for Escherichia coli - Support for any encoding, which means that any language-specific character with accents can be used for input
- Support for more arbitrary IDs used in laboratory information systems
- Small fix for preventing viruses being treated as bacteria
- Small fix for preventing contamination and lack of growth being treated as valid microorganisms
- Support for codes ending with
- Support for all abbreviations of antibiotics and antimycotics used by the Netherlands National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM)
- Added more abbreviations to the
antibiotics
data set - Reloaded original EUCAST master tables from 2019 (2020 was already available). This seems more reliable than the data we used from WHONET.
- Added generic CLSI rules for R/SI interpretation using
as.rsi()
for years 2010-2019 (thanks to Anthony Underwood)
Other
- Support for the upcoming
dplyr
version 1.0.0 - More robust assigning for classes
rsi
andmic
AMR
1.0.1
Changed
- Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
- Interpretation from MIC values (and disk zones) to R/SI can now be used with
mutate_at()
of thedplyr
package:yourdata %>% mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = "E. coli") yourdata %>% mutate_at(vars(antibiotic1:antibiotic25), as.rsi, mo = .$mybacteria)
- Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
- Added
uti
(as abbreviation of urinary tract infections) as argument toas.rsi()
, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs - Info printing in functions
eucast_rules()
,first_isolate()
,mdro()
andresistance_predict()
will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
AMR
1.0.0
This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
New
- Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 1 January 2020. This affects translation of MIC and disk zones using
as.rsi()
and inferred resistance and susceptibility usingeucast_rules()
. - The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt. This allows for machine reading these guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file can be found here.
- Support for LOINC and SNOMED codes
- Support for LOINC codes in the
antibiotics
data set. Useab_loinc()
to retrieve LOINC codes, or use a LOINC code for input in anyab_*
function:ab_loinc("ampicillin") #> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5" ab_name("21066-6") #> [1] "Ampicillin" ab_atc("21066-6") #> [1] "J01CA01"
- Support for SNOMED CT codes in the
microorganisms
data set. Usemo_snomed()
to retrieve SNOMED codes, or use a SNOMED code for input in anymo_*
function:mo_snomed("S. aureus") #> [1] 115329001 3092008 113961008 mo_name(115329001) #> [1] "Staphylococcus aureus" mo_gramstain(115329001) #> [1] "Gram-positive"
- Support for LOINC codes in the
Changes
- The
as.mo()
function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the functionclear_mo_history()
was removed. - Bugfix for some WHONET microorganism codes that were not interpreted correctly when using
as.rsi()
- Improvements for the algorithm used by
as.mo()
(and consequently allmo_*
functions, that useas.mo()
internally):- Support for missing spaces, e.g. in
as.mo("Methicillin-resistant S.aureus")
- Better support for determination of Salmonella biovars
- Speed improvements, especially for the G. species format (G for genus), like E. coli and K pneumoniae
- Support for more common codes used in laboratory information systems
- Support for missing spaces, e.g. in
- Input values for
as.disk()
limited to a maximum of 50 millimeters - Added a lifecycle state to every function, following the lifecycle circle of the
tidyverse
- For in
as.ab()
: support for drugs starting with "co-" like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey) - Changes to the
antibiotics
data set (thanks to Peter Dutey):- Added more synonyms to colistin, imipenem and piperacillin/tazobactam
- Moved synonyms Rifinah and Rimactazid from rifampicin (
RIF
) to rifampicin/isoniazid (RFI
). Please note that the combination rifampicin/isoniazid has no DDDs defined, so e.g.ab_ddd("Rimactazid")
will now returnNA
. - Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (
SMX
) to trimethoprim/sulfamethoxazole (SXT
)
Other
- Add a
CITATION
file - Full support for the upcoming R 4.0
- Removed unnecessary
AMR::
calls
AMR
0.9.0
Breaking
- Adopted Adeolu et al. (2016), PMID 27620848 for the
microorganisms
data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like Morganellaceae and Yersiniaceae). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations withmdro()
will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.- If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:
then please adjust this to:if (mo_family(somebugs) == "Enterobacteriaceae") ...
if (mo_order(somebugs) == "Enterobacterales") ...
- If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:
New
- Functions
susceptibility()
andresistance()
as aliases ofproportion_SI()
andproportion_R()
, respectively. These functions were added to make it more clear that "I" should be considered susceptible and not resistant.library(dplyr) example_isolates %>% group_by(bug = mo_name(mo)) %>% summarise(amoxicillin = resistance(AMX), amox_clav = resistance(AMC)) %>% filter(!is.na(amoxicillin) | !is.na(amox_clav))
- Support for a new MDRO guideline: Magiorakos AP, Srinivasan A et al. "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012).
- This is now the new default guideline for the
mdro()
function - The new Verbose mode (
mdro(...., verbose = TRUE)
) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents
- This is now the new default guideline for the
- Data set
antivirals
, containing all entries from the ATC J05 group with their DDDs for oral and parenteral treatment
Changes
- Improvements to algorithm in
as.mo()
:- Now allows "ou" where "au" should have been used and vice versa
- More intelligent way of coping with some consonants like "l" and "r"
- Added a score (a certainty percentage) to
mo_uncertainties()
, that is calculated using the Levenshtein distance:as.mo(c("Stafylococcus aureus", "staphylokok aureuz")) #> Warning: #> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them. #> Class 'mo' #> [1] B_STPHY_AURS B_STPHY_AURS mo_uncertainties() #> "Stafylococcus aureus" -> Staphylococcus aureus (B_STPHY_AURS, score: 95.2%) #> "staphylokok aureuz" -> Staphylococcus aureus (B_STPHY_AURS, score: 85.7%)
- Removed previously deprecated function
as.atc()
- this function was replaced byab_atc()
- Renamed all
portion_*
functions toproportion_*
. Allportion_*
functions are still available as deprecated functions, and will return a warning when used. - When running
as.rsi()
over a data set, it will now print the guideline that will be used if it is not specified by the user - Improvements for
eucast_rules()
:- Fix where Stenotrophomonas maltophilia would always become ceftazidime R (following EUCAST v3.1)
- Fix where Leuconostoc and Pediococcus would not always become glycopeptides R
- non-EUCAST rules in
eucast_rules()
are now applied first and not as last anymore. This is to improve the dependency on certain antibiotics for the official EUCAST rules. Please see?eucast_rules
.
- Fix for interpreting MIC values with
as.rsi()
where the input isNA
- Added "imi" and "imp" as allowed abbreviation for Imipenem (IPM)
- Fix for automatically determining columns with antibiotic results in
mdro()
andeucast_rules()
- Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the
antibiotics
data set - More robust way of determining valid MIC values
- Small changed to the
example_isolates
data set to better reflect reality - Added more microorganisms codes from laboratory systems (esp. species of Pseudescherichia and Rodentibacter)
- Added Gram-stain to
mo_info()
Other
- Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great Roxygen2, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.
- Change dependency on
clean
tocleaner
, as this package was renamed accordingly upon CRAN request - Added Dr. Sofia Ny as contributor
AMR
0.8.0
Breaking
- Determination of first isolates now excludes all 'unknown' microorganisms at default, i.e. microbial code
"UNKNOWN"
. They can be included with the new argumentinclude_unknown
:
For WHONET users, this means that all records/isolates with organism codefirst_isolate(..., include_unknown = TRUE)
"con"
(contamination) will be excluded at default, sinceas.mo("con") = "UNKNOWN"
. The function always shows a note with the number of 'unknown' microorganisms that were included or excluded. - For code consistency, classes
ab
andmo
will now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result inNA
:
This is important, because a value like# how it works in base R: x <- factor("A") x[1] <- "B" #> Warning message: #> invalid factor level, NA generated # how it now works similarly for classes 'mo' and 'ab': x <- as.mo("E. coli") x[1] <- "testvalue" #> Warning message: #> invalid microorganism code, NA generated
"testvalue"
could never be understood by e.g.mo_name()
, although the class would suggest a valid microbial code. - Function
freq()
has moved to a new package,clean
(CRAN link), since creating frequency tables actually does not fit the scope of this package. Thefreq()
function still works, since it is re-exported from theclean
package (which will be installed automatically upon updating thisAMR
package). - Renamed data set
septic_patients
toexample_isolates
New
-
Function
bug_drug_combinations()
to quickly get adata.frame
with the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed withmo_shortname()
at default:x <- bug_drug_combinations(example_isolates) #> NOTE: Using column `mo` as input for `col_mo`. x[1:4, ] #> mo ab S I R total #> 1 A. baumannii AMC 0 0 3 3 #> 2 A. baumannii AMK 0 0 0 0 #> 3 A. baumannii AMP 0 0 3 3 #> 4 A. baumannii AMX 0 0 3 3 #> NOTE: Use 'format()' on this result to get a publicable/printable format. # change the transformation with the FUN argument to anything you like: x <- bug_drug_combinations(example_isolates, FUN = mo_gramstain) #> NOTE: Using column `mo` as input for `col_mo`. x[1:4, ] #> mo ab S I R total #> 1 Gram-negative AMC 469 89 174 732 #> 2 Gram-negative AMK 251 0 2 253 #> 3 Gram-negative AMP 227 0 405 632 #> 4 Gram-negative AMX 227 0 405 632 #> NOTE: Use 'format()' on this result to get a publicable/printable format.
You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R
format()
function:format(x, combine_IR = FALSE)
-
Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for
portion_*
functions orcount_*
functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argumentonly_all_tested
(which defaults toFALSE
) replaces the oldalso_single_tested
and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on theportion
andcount
help pages), where the %SI is being determined:# -------------------------------------------------------------------- # only_all_tested = FALSE only_all_tested = TRUE # ----------------------- ----------------------- # Drug A Drug B include as include as include as include as # numerator denominator numerator denominator # -------- -------- ---------- ----------- ---------- ----------- # S or I S or I X X X X # R S or I X X X X # <NA> S or I X X - - # S or I R X X X X # R R - X - X # <NA> R - - - - # S or I <NA> X X - - # R <NA> - - - - # <NA> <NA> - - - - # --------------------------------------------------------------------
Since this is a major change, usage of the old
also_single_tested
will throw an informative error that it has been replaced byonly_all_tested
. -
tibble
printing support for classesrsi
,mic
,disk
,ab
mo
. When usingtibble
s containing antimicrobial columns, valuesS
will print in green, valuesI
will print in yellow and valuesR
will print in red. Microbial IDs (classmo
) will emphasise on the genus and species, not on the kingdom.# (run this on your own console, as this page does not support colour printing) library(dplyr) example_isolates %>% select(mo:AMC) %>% as_tibble()
Changed
- Many algorithm improvements for
as.mo()
(of which some led to additions to themicroorganisms
data set). Many thanks to all contributors that helped improving the algorithms.- Self-learning algorithm - the function now gains experience from previously determined microorganism IDs and learns from it (yielding 80-95% speed improvement for any guess after the first try)
- Big improvement for misspelled input
- These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
- Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology
- Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)
- Added support for Blastocystis
- Added support for 5,000 new fungi
- Added support for unknown yeasts and fungi
- Changed most microorganism IDs to improve readability. For example, the old code
B_ENTRC_FAE
could have been both E. faecalis and E. faecium. Its new code isB_ENTRC_FCLS
and E. faecium has becomeB_ENTRC_FACM
. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for Aerococcus urinae wasB_ARCCC_NAE
. This is nowB_AERCC_URIN
. IMPORTANT: Old microorganism IDs are still supported, but support will be dropped in a future version. Useas.mo()
on your old codes to transform them to the new format. Using functions from themo_*
family (likemo_name()
andmo_gramstain()
) on old codes, will throw a warning.
- More intelligent guessing for
as.ab()
, including bidirectional language support - Added support for the German national guideline (3MRGN/4MRGN) in the
mdro()
function, to determine multi-drug resistant organisms - Function
eucast_rules()
:- Fixed a bug for Yersinia pseudotuberculosis
- Added more informative errors and warnings
- Printed info now distinguishes between added and changes values
- Using Verbose mode (i.e.
eucast_rules(..., verbose = TRUE)
) returns more informative and readable output - Using factors as input now adds missing factors levels when the function changes antibiotic results
- Improved the internal auto-guessing function for determining antimicrobials in your data set (
AMR:::get_column_abx()
) - Removed class
atc
- usingas.atc()
is now deprecated in favour ofab_atc()
and this will return a character, not theatc
class anymore - Removed deprecated functions
abname()
,ab_official()
,atc_name()
,atc_official()
,atc_property()
,atc_tradenames()
,atc_trivial_nl()
- Fix and speed improvement for
mo_shortname()
- Fix for using
mo_*
functions where the coercion uncertainties and failures would not be available throughmo_uncertainties()
andmo_failures()
anymore - Deprecated the
country
argument ofmdro()
in favour of the already existingguideline
argument to support multiple guidelines within one country - The
name
ofRIF
is now Rifampicin instead of Rifampin - The
antibiotics
data set is now sorted by name and all cephalosporins now have their generation between brackets - Speed improvement for
guess_ab_col()
which is now 30 times faster for antibiotic abbreviations - Improved
filter_ab_class()
to be more reliable and to support 5th generation cephalosporins - Function
availability()
now usesportion_R()
instead ofportion_IR()
, to comply with EUCAST insights - Functions
age()
andage_groups()
now have ana.rm
argument to remove empty values - Renamed function
p.symbol()
top_symbol()
(the former is now deprecated and will be removed in a future version) - Using negative values for
x
inage_groups()
will now introduceNA
s and not return an error anymore - Fix for determining the system's language
- Fix for
key_antibiotics()
on foreign systems - Added 80 new LIS codes for microorganisms
- Relabeled the factor levels of
mdr_tb()
- Added more MIC factor levels (
as.mic()
)
Other
- Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
- Cleaned the coding style of every single syntax line in this package with the help of the
lintr
package
AMR
0.7.1
New
-
Function
rsi_df()
to transform adata.frame
to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functionscount_df()
andportion_df()
to immediately show resistance percentages and number of available isolates:septic_patients %>% select(AMX, CIP) %>% rsi_df() # antibiotic interpretation value isolates # 1 Amoxicillin SI 0.4442636 546 # 2 Amoxicillin R 0.5557364 683 # 3 Ciprofloxacin SI 0.8381831 1181 # 4 Ciprofloxacin R 0.1618169 228
-
Support for all scientifically published pathotypes of E. coli to date (that we could find). Supported are:
- AIEC (Adherent-Invasive E. coli)
- ATEC (Atypical Entero-pathogenic E. coli)
- DAEC (Diffusely Adhering E. coli)
- EAEC (Entero-Aggresive E. coli)
- EHEC (Entero-Haemorrhagic E. coli)
- EIEC (Entero-Invasive E. coli)
- EPEC (Entero-Pathogenic E. coli)
- ETEC (Entero-Toxigenic E. coli)
- NMEC (Neonatal Meningitis‐causing E. coli)
- STEC (Shiga-toxin producing E. coli)
- UPEC (Uropathogenic E. coli)
All these lead to the microbial ID of E. coli:
as.mo("UPEC") # B_ESCHR_COL mo_name("UPEC") # "Escherichia coli" mo_gramstain("EHEC") # "Gram-negative"
-
Function
mo_info()
as an analogy toab_info()
. Themo_info()
prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism -
Function
mo_synonyms()
to get all previously accepted taxonomic names of a microorganism
Changed
- Column names of output
count_df()
andportion_df()
are now lowercase - Fixed bug in translation of microorganism names
- Fixed bug in determining taxonomic kingdoms
- Algorithm improvements for
as.ab()
andas.mo()
to understand even more severely misspelled input - Function
as.ab()
now allows spaces for coercing antibiotics names - Added
ggplot2
methods for automatically determining the scale type of classesmo
andab
- Added names of object in the header in frequency tables, even when using pipes
- Prevented
"bacteria"
from getting coerced byas.ab()
because Bacterial is a brand name of trimethoprim (TMP) - Fixed a bug where setting an antibiotic would not work for
eucast_rules()
andmdro()
- Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
- Removed
latest_annual_release
from thecatalogue_of_life_version()
function - Removed antibiotic code
PVM1
from theantibiotics
data set as this was a duplicate ofPME
- Fixed bug where not all old taxonomic names would be printed, when using a vector as input for
as.mo()
- Manually added Trichomonas vaginalis from the kingdom of Protozoa, which is missing from the Catalogue of Life
- Small improvements to
plot()
andbarplot()
for MIC and RSI classes - Allow Catalogue of Life IDs to be coerced by
as.mo()
Other
- Fixed a note thrown by CRAN tests
AMR
0.7.0
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 withas.mic()
), a disk diffusion value (created with the newas.disk()
) or on a complete date set containing columns with MIC or disk diffusion values. - Function
mo_name()
as alias ofmo_fullname()
- Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (
mdr_tb()
) and added a new vignette about MDR. Read this tutorial here on our website.
Changed
- Fixed a critical bug in
first_isolate()
where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1. - Fixed a bug in
eucast_rules()
where antibiotics from WHONET software would not be recognised - Completely reworked the
antibiotics
data set:- 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
- Column
- 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
andatc_trivial_nl
have been removed - All
atc_*
functions are superseded byab_*
functions - All output will be translated by using an included translation file which can be viewed here
- All entries now have 3 different identifiers:
- Improvements to plotting AMR results with
ggplot_rsi()
:- New argument
colours
to set the bar colours - New arguments
title
,subtitle
,caption
,x.title
andy.title
to set titles and axis descriptions
- New argument
- Improved intelligence of looking up antibiotic columns in a 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 theas.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()
andcount_df()
this means that their new argumentcombine_SI
is TRUE at default. Our plotting functionggplot_rsi()
also reflects this change since it usescount_df()
internally. - The
age()
function gained a new argumentexact
to determine ages with decimals - Removed deprecated functions
guess_mo()
,guess_atc()
,EUCAST_rules()
,interpretive_reading()
,rsi()
- Frequency tables (
freq()
):- speed improvement for microbial IDs
- fixed factor level names for R Markdown
- when all values are unique it now shows a message instead of a warning
- support for boxplots:
septic_patients %>% freq(age) %>% boxplot() # grouped boxplots: septic_patients %>% group_by(hospital_id) %>% freq(age) %>% boxplot()
- Removed all hardcoded EUCAST rules and replaced them with a new reference file which can be viewed here
- 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+ - Fix for
freq()
for when all values areNA
- Fix for
first_isolate()
for when dates are missing - Improved speed of
guess_ab_col()
- Function
as.mo()
now gently interprets any number of whitespace characters (like tabs) as one space - Function
as.mo()
now returnsUNKNOWN
for"con"
(WHONET ID of 'contamination') and returnsNA
for"xxx"
(WHONET ID of 'no growth') - Small algorithm fix for
as.mo()
- Removed viruses from data set
microorganisms.codes
and cleaned it up - Fix for
mo_shortname()
where species would not be determined correctly
Other
- Support for R 3.6.0 and later by providing support for staged install
AMR
0.6.1
Changed
- Fixed a critical bug when using
eucast_rules()
withverbose = TRUE
- Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy
AMR
0.6.0
New website!
We've got a 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 arguments
- Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more.
New
- BREAKING: removed deprecated functions, arguments and references to 'bactid'. Use
as.mo()
to identify an MO code. - Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The
microorganisms
data set now contains:-
All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa
-
All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales (covering at least like all species of Aspergillus, Candida, Pneumocystis, Saccharomyces and Trichophyton)
-
All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like Strongyloides and Taenia)
-
All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed
-
The responsible author(s) and year of scientific publication
This data is updated annually - check the included version with the new function
catalogue_of_life_version()
. -
Due to this change, some
mo
codes changed (e.g. Streptococcus changed fromB_STRPTC
toB_STRPT
). A translation table is used internally to support older microorganism IDs, so users will not notice this difference. -
New function
mo_rank()
for the taxonomic rank (genus, species, infraspecies, etc.) -
New function
mo_url()
to get the direct URL of a species from the Catalogue of Life
-
- Support for data from WHONET and EARS-Net (European Antimicrobial Resistance Surveillance Network):
- Exported files from WHONET can be read and used in this package. For functions like
first_isolate()
andeucast_rules()
, all arguments will be filled in automatically. - This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the
antibiotics
data set now contains a columnears_net
. - The function
as.mo()
now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to themicroorganisms.codes
data set.
- Exported files from WHONET can be read and used in this package. For functions like
- New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:
Thefilter_aminoglycosides() filter_carbapenems() filter_cephalosporins() filter_1st_cephalosporins() filter_2nd_cephalosporins() filter_3rd_cephalosporins() filter_4th_cephalosporins() filter_fluoroquinolones() filter_glycopeptides() filter_macrolides() filter_tetracyclines()
antibiotics
data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in theantibiotics
data set. For example:septic_patients %>% filter_glycopeptides(result = "R") # Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R septic_patients %>% filter_glycopeptides(result = "R", scope = "all") # Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R
- All
ab_*
functions are deprecated and replaced byatc_*
functions:
These functions useab_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()
as.atc()
internally. The oldatc_property
has been renamedatc_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 classatc
or must be coerable to this class. Properties of these classes should start with the same class name, analogous toas.mo()
and e.g.mo_genus
. - New functions
set_mo_source()
andget_mo_source()
to use your own predefined MO codes as input foras.mo()
and consequently allmo_*
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, usingas.mo()
. This latter function will now only show a maximum of 10 uncoerced values and will refer tomo_failures()
. - New function
mo_uncertainties()
to review values that could be coerced to a valid MO code usingas.mo()
, but with uncertainty. - New function
mo_renamed()
to get a list of all returned values fromas.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 AMR data analysis per age group. - New function
ggplot_rsi_predict()
as well as the base Rplot()
function can now be used for resistance prediction calculated withresistance_predict()
:x <- resistance_predict(septic_patients, col_ab = "amox") plot(x) ggplot_rsi_predict(x)
- Functions
filter_first_isolate()
andfilter_first_weighted_isolate()
to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
is equal to:septic_patients %>% filter_first_isolate(...) # or filter_first_isolate(septic_patients, ...)
septic_patients %>% mutate(only_firsts = first_isolate(septic_patients, ...)) %>% filter(only_firsts == TRUE) %>% select(-only_firsts)
- New function
availability()
to check the number of available (non-empty) results in adata.frame
- 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
- Function
eucast_rules()
:- Updated EUCAST Clinical breakpoints to version 9.0 of 1 January 2019, the data set
septic_patients
now reflects these changes - 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)
- New info is returned when running this function, stating exactly what has been changed or added. Use
eucast_rules(..., verbose = TRUE)
to get a data set with all changed per bug and drug combination.
- Updated EUCAST Clinical breakpoints to version 9.0 of 1 January 2019, the data set
- Removed data sets
microorganisms.oldDT
,microorganisms.prevDT
,microorganisms.unprevDT
andmicroorganismsDT
since they were no longer needed and only contained info already available in themicroorganisms
data set - Added 65 antibiotics to the
antibiotics
data set, from the Pharmaceuticals Community Register of the European Commission - Removed columns
atc_group1_nl
andatc_group2_nl
from theantibiotics
data set - Functions
atc_ddd()
andatc_groups()
have been renamedatc_online_ddd()
andatc_online_groups()
. The old functions are deprecated and will be removed in a future version. - Function
guess_mo()
is now deprecated in favour ofas.mo()
and will be removed in future versions - Function
guess_atc()
is now deprecated in favour ofas.atc()
and will be removed in future versions - Improvements for
as.mo()
:- Now handles incorrect spelling, like
i
instead ofy
andf
instead ofph
:# mo_fullname() uses as.mo() internally mo_fullname("Sthafilokockus aaureuz") #> [1] "Staphylococcus aureus" mo_fullname("S. klossi") #> [1] "Staphylococcus kloosii"
- Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default
allow_uncertain = TRUE
is equal to uncertainty level 2. Run?as.mo
for more info about these levels.
Using# equal: as.mo(..., allow_uncertain = TRUE) as.mo(..., allow_uncertain = 2) # also equal: as.mo(..., allow_uncertain = FALSE) as.mo(..., allow_uncertain = 0)
as.mo(..., allow_uncertain = 3)
could lead to very unreliable results. - Implemented the latest publication of Becker et al. (2019), for categorising coagulase-negative Staphylococci
- All microbial IDs that found are now saved to a local file
~/.Rhistory_mo
. Use the new functionclean_mo_history()
to delete this file, which resets the algorithms. - Incoercible results will now be considered 'unknown', MO code
UNKNOWN
. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:mo_genus("qwerty", language = "es") # Warning: # one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it. #> [1] "(género desconocido)"
- Fix for vector containing only empty values
- Finds better results when input is in other languages
- Better handling for subspecies
- Better handling for Salmonellae, especially the 'city like' serovars like Salmonella London
- Understanding of highly virulent E. coli strains like EIEC, EPEC and STEC
- There will be looked for uncertain results at default - these results will be returned with an informative warning
- Manual (help page) 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
- Now handles incorrect spelling, like
- 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 (argument
col_patientid
), when this argument was left blank - Will now use a column named like "key(...)ab" or "key(...)antibiotics" for the key antibiotics (argument
col_keyantibiotics()
), when this argument was left blank - Removed argument
output_logical
, the function will now always return a logical value - Renamed argument
filter_specimen
tospecimen_group
, although usingfilter_specimen
will still work
- Fixed a bug where distances between dates would not be calculated right - in the
- A note to the manual pages of the
portion
functions, that low counts can influence the outcome and that theportion
functions may camouflage this, since they only return the portion (albeit being dependent on theminimum
argument) - Merged data sets
microorganisms.certe
andmicroorganisms.umcg
intomicroorganisms.codes
- Function
mo_taxonomy()
now contains the kingdom too - Reduce false positives for
is.rsi.eligible()
using the newthreshold
argument - New colours for
scale_rsi_colours()
- Summaries of class
mo
will now return the top 3 and the unique count, e.g. usingsummary(mo)
- Small text updates to summaries of class
rsi
andmic
- Function
as.rsi()
:- Now gives a warning when inputting MIC values
- Now accepts high and low resistance:
"HIGH S"
will returnS
- Frequency tables (
freq()
function):- Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
# Determine genus of microorganisms (mo) in `septic_patients` data set: # OLD WAY septic_patients %>% mutate(genus = mo_genus(mo)) %>% freq(genus) # NEW WAY septic_patients %>% freq(mo_genus(mo)) # Even supports grouping variables: septic_patients %>% group_by(gender) %>% freq(mo_genus(mo))
- Header info is now available as a list, with the
header
function - The argument
header
is now set toTRUE
at default, even for markdown - Added header info for class
mo
to show unique count of families, genera and species - Now honours the
decimal.mark
setting, which just likeformat
defaults togetOption("OutDec")
- The new
big.mark
argument will at default be","
whendecimal.mark = "."
and"."
otherwise - Fix for header text where all observations are
NA
- New argument
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
- Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
- Function
scale_y_percent()
now contains thelimits
argument - Automatic argument filling for
mdro()
,key_antibiotics()
andeucast_rules()
- Updated examples for resistance prediction (
resistance_predict()
function) - Fix for
as.mic()
to support more values ending in (several) zeroes - if using different lengths of pattern and x in
%like%
, it will now return the call
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
- Function
count_all
to get all available isolates (that like allportion_*
andcount_*
functions also supportssummarise
andgroup_by
), the oldn_rsi
is now an alias ofcount_all
- Function
get_locale
to determine language for language-dependent output for somemo_*
functions. This is now the default value for theirlanguage
argument, by which the system language will be used at default. - Data sets
microorganismsDT
,microorganisms.prevDT
,microorganisms.unprevDT
andmicroorganisms.oldDT
to improve the speed ofas.mo
. They are for reference only, since they are primarily for internal use ofas.mo
. - Function
read.4D
to read from the 4D database of the MMB department of the UMCG - Functions
mo_authors
andmo_year
to get specific values about the scientific reference of a taxonomic entry
Changed
- Functions
MDRO
,BRMO
,MRGN
andEUCAST_exceptional_phenotypes
were renamed tomdro
,brmo
,mrgn
andeucast_exceptional_phenotypes
EUCAST_rules
was renamed toeucast_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, https://www.eucast.org/clinical_breakpoints/ (see Source of the function)
- New argument
rules
to specify which rules should be applied (expert rules, breakpoints, others or all) - New argument
verbose
which can be set toTRUE
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 argument
pipe
for piperacillin (J01CA12), also to themdro
function - Small fixes to EUCAST clinical breakpoint rules
- Added column
kingdom
to the microorganisms data set, and functionmo_kingdom
to look up values - Tremendous speed improvement for
as.mo
(and subsequently allmo_*
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 allmo_*
wrappers) now supports genus abbreviations with "species" attachedas.mo("E. species") # B_ESCHR mo_fullname("E. spp.") # "Escherichia species" as.mo("S. spp") # B_STPHY mo_fullname("S. species") # "Staphylococcus species"
- Added argument
combine_IR
(TRUE/FALSE) to functionsportion_df
andcount_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 argument
also_single_tested
forportion_*
andcount_*
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 argumentminimum
- Functions
as.mo
,as.rsi
,as.mic
,as.atc
andfreq
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 argument
na
, to choose which character to print for empty values - New argument
header
to turn the header info off (default whenmarkdown = TRUE
) - New argument
title
to manually setbthe title of the frequency table
- Support for grouping variables, test with:
first_isolate
now tries to find columns to use as input when arguments are left blank- Improvements for MDRO algorithm (function
mdro
) - Data set
septic_patients
is now adata.frame
, not a tibble anymore - Removed diacritics from all authors (columns
microorganisms$ref
andmicroorganisms.old$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 fortop_freq()
ggplot_rsi
andscale_y_percent
havebreaks
argument- 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
, whensum(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 onas.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 toImport
field) sinceportion_df
andcount_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 setmicroorganisms.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"
- Taxonomic names:
-
Functions
count_R
,count_IR
,count_I
,count_SI
andcount_S
to selectively count resistant or susceptible isolates- Extra function
count_df
(which works likeportion_df
) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables
- Extra function
-
Function
is.rsi.eligible
to check for columns that have valid antimicrobial results, but do not have thersi
class yet. Transform the columns of your raw data with:data %>% mutate_if(is.rsi.eligible, as.rsi)
-
Functions
as.mo
andis.mo
as replacements foras.bactid
andis.bactid
(since themicrooganisms
data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. Theas.mo
function determines microbial IDs using intelligent rules: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 argument
reference_df
foras.mo
, so users can supply their own microbial IDs, name or codes as a reference table -
Renamed all previous references to
bactid
tomo
, like:- Column names inputs of
EUCAST_rules
,first_isolate
andkey_antibiotics
- Column names of datasets
microorganisms
andseptic_patients
- All old syntaxes will still work with this version, but will throw warnings
- Column names inputs of
-
Function
labels_rsi_count
to print datalabels on a RSIggplot2
model -
Functions
as.atc
andis.atc
to transform/look up antibiotic ATC codes as defined by the WHO. The existing functionguess_atc
is now an alias ofas.atc
. -
Function
ab_property
and its aliases:ab_name
,ab_tradenames
,ab_certe
,ab_umcg
andab_trivial_nl
-
Introduction to AMR as a vignette
-
Removed clipboard functions as it violated the CRAN policy
-
Renamed
septic_patients$sex
toseptic_patients$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 themicroorganisms
data set - Added arguments
minimum
andas_percent
toportion_df
- Support for quasiquotation in the functions series
count_*
andportions_*
, andn_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
andgeom_rsi
so they can cope withcount_df
. The newfun
argument has valueportion_df
at default, but can be set tocount_df
. - Fix for
ggplot_rsi
when theggplot2
package was not loaded - Added datalabels function
labels_rsi_count
toggplot_rsi
- Added possibility to set any argument to
geom_rsi
(andggplot_rsi
) so you can set your own preferences - Fix for joins, where predefined suffices would not be honoured
- Added argument
quote
to thefreq
function - Added generic function
diff
for frequency tables - Added longest en shortest character length in the frequency table (
freq
) header of classcharacter
- Support for types (classes) list and matrix for
freq
For lists, subsetting is possible:my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2)) freq(my_matrix)
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 functionsportion_R
,portion_IR
,portion_I
,portion_SI
andportion_S
to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the oldrsi
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
- New function
- 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
andtheme_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
- New functions
- Determining bacterial ID:
- New functions
as.bactid
andis.bactid
to transform/ look up microbial ID's. - The existing function
guess_bactid
is now an alias ofas.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
- New functions
- For convience, new descriptive statistical functions
kurtosis
andskewness
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 aschisq.test
Functionratio
to transform a vector of values to a preset ratioFor example:ratio(c(10, 500, 10), ratio = "1:2:1")
would return130, 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
andclipboard_export
as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use theclipr
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
andplot
to use a frequency table as input:hist(freq(df$age))
- Support for
as.vector
,as.data.frame
,as_tibble
andformat
- Support for quasiquotation:
freq(mydata, mycolumn)
is the same asmydata %>% 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 arguments 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
andrsi
classes now returns all values - usefreq
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.frame
s with altered console printing to make it look like a frequency table. Because of this, the argumenttoConsole
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 columnbactid
now has the new class"bactid"
- Small improvements to the
microorganisms
dataset (especially for Salmonella) and the columnbactid
now has the new class"bactid"
- Combined MIC/RSI values will now be coerced by the
rsi
andmic
functions:as.rsi("<=0.002; S")
will returnS
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
andmic
do not add the attributepackage.version
anymore - Added
"groups"
option foratc_property(..., property)
. It will return a vector of the ATC hierarchy as defined by the WHO. The new functionatc_groups
is a convenient wrapper around this. - Build-in host check for
atc_property
as it requires the host set byurl
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 thedplyr
package v0.7.5 and above - Support for empty values and for 1 or 2 columns as input for
guess_bactid
(now calledas.bactid
)- So
yourdata %>% select(genus, species) %>% as.bactid()
now also works
- So
- 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 withdplyr::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
andMRGN
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
tibble
s anddata.table
s
Changed
- Fixed
rsi
class for vectors that contain only invalid antimicrobial interpretations - Renamed dataset
ablist
toantibiotics
- Renamed dataset
bactlist
tomicroorganisms
- 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 arguments of functions
first_isolate
andEUCAST_rules
column names are now case-insensitive - Functions
as.rsi
andas.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
andmic
classes
AMR
0.1.0
- First submission to CRAN.