freq() has moved to a new package, clean (CRAN link). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the freq() function. The clean package is available on CRAN and will be installed automatically when updating the AMR package, that now imports it. In a later stage, the skewness() and kurtosis() functions will be moved to the clean package too.Determination of first isolates now excludes all ‘unknown’ microorganisms at default, i.e. microbial code "UNKNOWN". They can be included with the new parameter include_unknown:
For WHONET users, this means that all records with organism code "con" (contamination) will be excluded at default, since as.mo("con") = "UNKNOWN". The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.
Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for portion_* functions or count_* functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter only_all_tested (which defaults to FALSE) replaces the old also_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 the portion and count help pages), where the %SI is being determined:
# -------------------------------------------------------------------------
# only_all_tested = FALSE only_all_tested = TRUE
# Antibiotic Antibiotic ----------------------- -----------------------
# A B include as include as include as include as
# numerator denominator numerator denominator
# ---------- ---------- ---------- ----------- ---------- -----------
# S S X X X X
# I S X X X X
# R S X X X X
# not tested S X X - -
# S I X X X X
# I I X X X X
# R I X X X X
# not tested I X X - -
# S R X X X X
# I R X X X X
# R R - X - X
# not tested R - - - -
# S not tested X X - -
# I not tested X X - -
# R not tested - - - -
# not tested not tested - - - -
# -------------------------------------------------------------------------Since this is a major change, usage of the old also_single_tested will throw an informative error that it has been replaced by only_all_tested.
eucast_rules()
eucast_rules(..., verbose = TRUE)) returns more informative and readable outputAdded tibble printing support for classes rsi, mic, disk, ab mo. When using tibbles containing antibiotic columns, values S will print in green, values I will print in yellow and values R will print in red. Microbial IDs (class mo) will emphasise on the genus and species, not on the kingdom.
atc - using as.atc() is now deprecated in favour of ab_atc() and this will return a character, not the atc class anymoreabname(), ab_official(), atc_name(), atc_official(), atc_property(), atc_tradenames(), atc_trivial_nl()
mo_shortname()
as.mo():
microorganisms data set to contain the latest taxonomic data from the IJSEM journal (now up to date until August 2019)microorganisms data setmo_* functions where the coercion uncertainties and failures would not be available through mo_uncertainties() and mo_failures() anymorecountry parameter of mdro() in favour of the already existing guideline parameter to support multiple guidelines within one countryname of RIF is now Rifampicin instead of Rifampinantibiotics data set is now sorted by name and all cephalosporins now have their generation between bracketsguess_ab_col() which is now 30 times faster for antibiotic abbreviationsfilter_ab_class() to be more reliable and to support 5th generation cephalosporinsClasses ab and mo will now be preserved in any subsetting
Function rsi_df() to transform a data.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 functions count_df() and portion_df() to immediately show resistance percentages and number of available isolates:
Support for all scientifically published pathotypes of E. coli to date (that we could find). Supported are:
All these lead to the microbial ID of E. coli:
mo_info() as an analogy to ab_info(). The mo_info() prints a list with the full taxonomy, authors, and the URL to the online database of a microorganismFunction mo_synonyms() to get all previously accepted taxonomic names of a microorganism
count_df() and portion_df() are now lowercaseas.ab() and as.mo() to understand even more severely misspelled inputas.ab() now allows spaces for coercing antibiotics namesggplot2 methods for automatically determining the scale type of classes mo and ab
"bacteria" from getting coerced by as.ab() because Bacterial is a brand name of trimethoprim (TMP)eucast_rules() and mdro()
latest_annual_release from the catalogue_of_life_version() functionPVM1 from the antibiotics data set as this was a duplicate of PME
as.mo()
plot() and barplot() for MIC and RSI classesas.mo()
as.rsi() on an MIC value (created with as.mic()), a disk diffusion value (created with the new as.disk()) or on a complete date set containing columns with MIC or disk diffusion values.mo_name() as alias of mo_fullname()
mdr_tb()) and added a new vignette about MDR. Read this tutorial here on our website.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.eucast_rules() where antibiotics from WHONET software would not be recognisedantibiotics data set:
ab contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this packageatc contains the ATC code, used by WHO/WHOCCcid contains the CID code (Compound ID), used by PubChemAMX for amoxicillinatc_certe, ab_umcg and atc_trivial_nl have been removedatc_* functions are superceded by ab_* functionsAll 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.ggplot_rsi():
colours to set the bar colourstitle, subtitle, caption, x.title and y.title to set titles and axis descriptionsguess_ab_col()
microorganisms.old data set, which leads to better results finding when using the as.mo() functionportion_df() and count_df() this means that their new parameter combine_SI is TRUE at default. Our plotting function ggplot_rsi() also reflects this change since it uses count_df() internally.age() function gained a new parameter exact to determine ages with decimalsguess_mo(), guess_atc(), EUCAST_rules(), interpretive_reading(), rsi()
freq()):
support for boxplots:
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.age_groups(), to let groups of fives and tens end with 100+ instead of 120+freq() for when all values are NA
first_isolate() for when dates are missingguess_ab_col()
as.mo() now gently interprets any number of whitespace characters (like tabs) as one spaceas.mo() now returns UNKNOWN for "con" (WHONET ID of ‘contamination’) and returns NA for "xxx"(WHONET ID of ‘no growth’)as.mo()
microorganisms.codes and cleaned it upFix for mo_shortname() where species would not be determined correctly
eucast_rules() with verbose = TRUE
New website!
We’ve got a new website: https://msberends.gitlab.io/AMR (built with the great pkgdown)
as.mo() to identify an MO code.microorganisms data set now contains:
The responsible author(s) and year of scientific publication
This data is updated annually - check the included version with the new functioncatalogue_of_life_version().mo codes changed (e.g. Streptococcus changed from B_STRPTC to B_STRPT). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.mo_rank() for the taxonomic rank (genus, species, infraspecies, etc.)mo_url() to get the direct URL of a species from the Catalogue of Lifefirst_isolate() and eucast_rules(), all parameters will be filled in automatically.antibiotics data set now contains a column ears_net.as.mo() now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to the microorganisms.codes data set.New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:
filter_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()The 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 the antibiotics data set. For example:
All ab_* functions are deprecated and replaced by atc_* functions:
ab_property -> atc_property()
ab_name -> atc_name()
ab_official -> atc_official()
ab_trivial_nl -> atc_trivial_nl()
ab_certe -> atc_certe()
ab_umcg -> atc_umcg()
ab_tradenames -> atc_tradenames()as.atc() internally. The old atc_property has been renamed atc_online_property(). This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class atc or must be coerable to this class. Properties of these classes should start with the same class name, analogous to as.mo() and e.g. mo_genus.set_mo_source() and get_mo_source() to use your own predefined MO codes as input for as.mo() and consequently all mo_* functionsdplyr version 0.8.0guess_ab_col() to find an antibiotic column in a tablemo_failures() to review values that could not be coerced to a valid MO code, using as.mo(). This latter function will now only show a maximum of 10 uncoerced values and will refer to mo_failures().mo_uncertainties() to review values that could be coerced to a valid MO code using as.mo(), but with uncertainty.mo_renamed() to get a list of all returned values from as.mo() that have had taxonomic renamingage() to calculate the (patients) age in yearsage_groups() to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.New function ggplot_rsi_predict() as well as the base R plot() function can now be used for resistance prediction calculated with resistance_predict():
Functions filter_first_isolate() and filter_first_weighted_isolate() to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
is equal to:
availability() to check the number of available (non-empty) results in a data.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.
eucast_rules():
septic_patients now reflects these changeseucast_rules(..., verbose = TRUE) to get a data set with all changed per bug and drug combination.microorganisms.oldDT, microorganisms.prevDT, microorganisms.unprevDT and microorganismsDT since they were no longer needed and only contained info already available in the microorganisms data setantibiotics data set, from the Pharmaceuticals Community Register of the European Commissionatc_group1_nl and atc_group2_nl from the antibiotics data setatc_ddd() and atc_groups() have been renamed atc_online_ddd() and atc_online_groups(). The old functions are deprecated and will be removed in a future version.guess_mo() is now deprecated in favour of as.mo() and will be removed in future versionsguess_atc() is now deprecated in favour of as.atc() and will be removed in future versionsas.mo():
Now handles incorrect spelling, like i instead of y and f instead of ph:
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.
# 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.~/.Rhistory_mo. Use the new function clean_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:
first_isolate():
septic_patients data set this yielded a difference of 0.15% more isolatescol_patientid), when this parameter was left blankcol_keyantibiotics()), when this parameter was left blankoutput_logical, the function will now always return a logical valuefilter_specimen to specimen_group, although using filter_specimen will still workportion functions, that low counts can influence the outcome and that the portion functions may camouflage this, since they only return the portion (albeit being dependent on the minimum parameter)microorganisms.certe and microorganisms.umcg into microorganisms.codes
mo_taxonomy() now contains the kingdom toois.rsi.eligible() using the new threshold parameterscale_rsi_colours()
mo will now return the top 3 and the unique count, e.g. using summary(mo)
rsi and mic
as.rsi():
"HIGH S" will return S
freq() function):
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
header functionheader is now set to TRUE at default, even for markdownmo to show unique count of families, genera and speciesdecimal.mark setting, which just like format defaults to getOption("OutDec")
big.mark parameter will at default be "," when decimal.mark = "." and "." otherwiseNA
droplevels to exclude empty factor levels when input is a factorselect() on frequency tablesscale_y_percent() now contains the limits parametermdro(), key_antibiotics() and eucast_rules()
resistance_predict() function)as.mic() to support more values ending in (several) zeroes%like%, it will now return the callcount_all to get all available isolates (that like all portion_* and count_* functions also supports summarise and group_by), the old n_rsi is now an alias of count_all
get_locale to determine language for language-dependent output for some mo_* functions. This is now the default value for their language parameter, by which the system language will be used at default.microorganismsDT, microorganisms.prevDT, microorganisms.unprevDT and microorganisms.oldDT to improve the speed of as.mo. They are for reference only, since they are primarily for internal use of as.mo.read.4D to read from the 4D database of the MMB department of the UMCGmo_authors and mo_year to get specific values about the scientific reference of a taxonomic entryMDRO, BRMO, MRGN and EUCAST_exceptional_phenotypes were renamed to mdro, brmo, mrgn and eucast_exceptional_phenotypes
EUCAST_rules was renamed to eucast_rules, the old function still exists as a deprecated functioneucast_rules function:
rules to specify which rules should be applied (expert rules, breakpoints, others or all)verbose which can be set to TRUE to get very specific messages about which columns and rows were affectedseptic_patients now reflects these changespipe for piperacillin (J01CA12), also to the mdro functionkingdom to the microorganisms data set, and function mo_kingdom to look up valuesas.mo (and subsequently all mo_* functions), as empty values wil be ignored a priori
as.mo will return NAFunction as.mo (and all mo_* wrappers) now supports genus abbreviations with “species” attached
combine_IR (TRUE/FALSE) to functions portion_df and count_df, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)portion_*(..., as_percent = TRUE) when minimal number of isolates would not be metalso_single_tested for portion_* and count_* functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see ?portion
portion_* functions now throws a warning when total available isolate is below parameter minimum
as.mo, as.rsi, as.mic, as.atc and freq will not set package name as attribute anymorefreq():
Support for grouping variables, test with:
Support for (un)selecting columns:
hms::is.hms
difftime
na, to choose which character to print for empty valuesheader to turn the header info off (default when markdown = TRUE)title to manually setbthe title of the frequency tablefirst_isolate now tries to find columns to use as input when parameters are left blankmdro)septic_patients is now a data.frame, not a tibble anymoremicroorganisms$ref and microorganisms.old$ref) to comply with CRAN policy to only allow ASCII charactersmo_property not working properlyeucast_rules where some Streptococci would become ceftazidime R in EUCAST rule 4.5mo, useful for top_freq()
ggplot_rsi and scale_y_percent have breaks parameteras.mo:
"CRS" -> Stenotrophomonas maltophilia
"CRSM" -> Stenotrophomonas maltophilia
"MSSA" -> Staphylococcus aureus
"MSSE" -> Staphylococcus epidermidis
join functionsis.rsi.eligible, now 15-20 times fasterg.test, when sum(x) is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggestedab_name will try to fall back on as.atc when no results are foundPercentages will now will rounded more logically (e.g. in freq function)
microorganisms now contains all microbial taxonomic data from ITIS (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set microorganisms.old contains all previously known taxonomic names from those kingdoms.mo_property:
mo_phylum, mo_class, mo_order, mo_family, mo_genus, mo_species, mo_subspecies
mo_fullname, mo_shortname
mo_type, mo_gramstain
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:
count_R, count_IR, count_I, count_SI and count_S to selectively count resistant or susceptible isolates
count_df (which works like portion_df) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variablesis.rsi.eligible to check for columns that have valid antimicrobial results, but do not have the rsi class yet. Transform the columns of your raw data with: data %>% mutate_if(is.rsi.eligible, as.rsi)
Functions as.mo and is.mo as replacements for as.bactid and is.bactid (since the microoganisms data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The as.mo function determines microbial IDs using 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_GRAAnd 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:
reference_df for as.mo, so users can supply their own microbial IDs, name or codes as a reference tablebactid to mo, like:
EUCAST_rules, first_isolate and key_antibiotics
microorganisms and septic_patients
labels_rsi_count to print datalabels on a RSI ggplot2 modelFunctions as.atc and is.atc to transform/look up antibiotic ATC codes as defined by the WHO. The existing function guess_atc is now an alias of as.atc.
ab_property and its aliases: ab_name, ab_tradenames, ab_certe, ab_umcg and ab_trivial_nl
Renamed septic_patients$sex to septic_patients$gender
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.:
first_isolate, rows will be ignored when there’s no species availableratio is now deprecated and will be removed in a future release, as it is not really the scope of this packageas.mic for values ending in zeroes after a real numbermicroorganisms.umcg data setprevalence column to the microorganisms data setminimum and as_percent to portion_df
Support for quasiquotation in the functions series count_* and portions_*, and n_rsi. This allows to check for more than 2 vectors or columns.
ggplot_rsi and geom_rsi so they can cope with count_df. The new fun parameter has value portion_df at default, but can be set to count_df.ggplot_rsi when the ggplot2 package was not loadedlabels_rsi_count to ggplot_rsi
geom_rsi (and ggplot_rsi) so you can set your own preferencesquote to the freq functiondiff for frequency tablesfreq) header of class character
Support for types (classes) list and matrix for freq
For lists, subsetting is possible:
rsi_df was removed in favour of new functions portion_R, portion_IR, portion_I, portion_SI and portion_S to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old rsi function. The old function still works, but is deprecated.
portion_df to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variablesggplot2
geom_rsi, facet_rsi, scale_y_percent, scale_rsi_colours and theme_rsi
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?ggplot_rsi
as.bactid and is.bactid to transform/ look up microbial ID’s.guess_bactid is now an alias of as.bactid
kurtosis and skewness that are lacking in base R - they are generic functions and have support for vectors, data.frames and matricesg.test to perform the Χ2 distributed G-test, which use is the same as chisq.test
ratio to transform a vector of values to a preset ratioratio(c(10, 500, 10), ratio = "1:2:1") would return 130, 260, 130%in% or %like% (and give them keyboard shortcuts), or to view the datasets that come with this packagep.symbol to transform p values to their related symbols: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
clipboard_import and clipboard_export as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the clipr package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)freq):
rsi (antimicrobial resistance) to use as inputtable to use as input: freq(table(x, y))
hist and plot to use a frequency table as input: hist(freq(df$age))
as.vector, as.data.frame, as_tibble and format
freq(mydata, mycolumn) is the same as mydata %>% freq(mycolumn)
top_freq function to return the top/below n items as vectoroptions(max.print.freq = n) where n is your preset valueresistance_predict and added more examplesseptic_patients data set to better reflect the realitymic and rsi classes now returns all values - use freq to check distributionskey_antibiotics function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABsabname function%like% now supports multiple patternsdata.frames with altered console printing to make it look like a frequency table. Because of this, the parameter toConsole is not longer needed.freq where the class of an item would be lostseptic_patients dataset and the column bactid now has the new class "bactid"
microorganisms dataset (especially for Salmonella) and the column bactid now has the new class "bactid"
rsi and mic functions:
as.rsi("<=0.002; S") will return S
as.mic("<=0.002; S") will return <=0.002
as.mic("<= 0.002") now worksrsi and mic do not add the attribute package.version anymore"groups" option for atc_property(..., property). It will return a vector of the ATC hierarchy as defined by the WHO. The new function atc_groups is a convenient wrapper around this.atc_property as it requires the host set by url to be responsivefirst_isolate algorithm to exclude isolates where bacteria ID or genus is unavailable924b62) from the dplyr package v0.7.5 and aboveguess_bactid (now called as.bactid)
yourdata %>% select(genus, species) %>% as.bactid() now also worksn_rsi to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise, see ?rsiguess_bactid to determine the ID of a microorganism based on genus/species or known abbreviations like MRSAguess_atc to determine the ATC of an antibiotic based on name, trade name, or known abbreviationsfreq to create frequency tables, with additional info in a headerMDRO to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines.
BRMO and MRGN are wrappers for Dutch and German guidelines, respectively"points" or "keyantibiotics", see ?first_isolate
tibbles and data.tablesrsi class for vectors that contain only invalid antimicrobial interpretationsablist to antibiotics
bactlist to microorganisms
antibiotics datasetmicroorganisms datasetseptic_patients
join functions%like% to make it case insensitivefirst_isolate and EUCAST_rules column names are now case-insensitiveas.rsi and as.mic now add the package name and version as attributesREADME.md with more examplestestthat package