56 KiB
Executable File
AMR 0.9.0.9007
Last updated: 27-Dec-2019
Changes
- Speed improvement for
as.mo()
(and consequently allmo_*
functions that useas.mo()
internally), especially for the G. species format (G for genus), like E. coli and K penumoniae - Input values for
as.disk()
limited to a maximum of 50 millimeters
Other
- Add a
CITATION
file
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 parameterinclude_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 parameteronly_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
parameter ofmdro()
in favour of the already existingguideline
parameter 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
parameter 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 superceded byab_*
functions -
All output will be translated by using an included translation file which can be viewed here.
Please create an issue in one of our repositories if you want additions in this file.
-
-
Improvements to plotting AMR results with
ggplot_rsi()
:- New parameter
colours
to set the bar colours - New parameters
title
,subtitle
,caption
,x.title
andy.title
to set titles and axis descriptions
- New parameter
-
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 parametercombine_SI
is TRUE at default. Our plotting functionggplot_rsi()
also reflects this change since it usescount_df()
internally. -
The
age()
function gained a new parameterexact
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.
Please create an issue in one of our repositories if you want changes in this file.
-
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 parameters
- Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.
New
- BREAKING: removed deprecated functions, parameters 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 parameters 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 antimicrobial resistance 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 (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
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
parameter) - 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
parameter - 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 parameter
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
parameter will at default be","
whendecimal.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
- Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
- Function
scale_y_percent()
now contains thelimits
parameter - Automatic parameter 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: https://gitlab.com/msberends/AMR
- 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
parameter, 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, 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 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 parameter
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 parameter
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 parameter
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 parameterminimum
- 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 parameter
na
, to choose which character to print for empty values - New parameter
header
to turn the header info off (default whenmarkdown = TRUE
) - New parameter
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 parameters 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
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
, 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 parameter
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 parameters
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
parameter 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 parameter to
geom_rsi
(andggplot_rsi
) so you can set your own preferences - Fix for joins, where predefined suffices would not be honoured
- Added parameter
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 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
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 parametertoConsole
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 parameters 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.