vignettes/datasets.Rmd
datasets.RmdNEWS.md
- AMR 1.7.1.9014AMR 1.7.1.9015betalactams() as additional antbiotic column selector and function filter_betalactams() as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.ggplot() method for resistance_predict()
+ggplot() method for resistance_predict()
Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info
ggplot() generics for classes <mic> and <disk>
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:
@@ -484,7 +484,7 @@
translate)plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesplot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion valuesmicroorganisms data setMaking this package independent of especially the tidyverse (e.g. packages dplyr and tidyr) 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:
freq() that was borrowed from the cleaner package was removed. Use cleaner::freq(), or run library("cleaner") before you use freq().freq() that was borrowed from the cleaner package was removed. Use cleaner::freq(), or run library("cleaner") before you use freq().mo or rsi in a tibble will no longer be in colour and printing rsi in a tibble will show the class <ord>, not <rsi> anymore. This is purely a visual effect.mo_* family (like mo_name() and mo_gramstain()) are noticeably slower when running on hundreds of thousands of rows.mo and ab now both also inherit class character, to support any data transformation. This change invalidates code that checks for class length == 1.This is important, because a value like "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. The freq() function still works, since it is re-exported from the clean package (which will be installed automatically upon updating this AMR package).
Function freq() has moved to a new package, clean (CRAN link), since creating frequency tables actually does not fit the scope of this package. The freq() function still works, since it is re-exported from the clean package (which will be installed automatically upon updating this AMR package).
Renamed data set septic_patients to example_isolates
age() function gained a new argument exact to determine ages with decimalsguess_mo(), guess_atc(), EUCAST_rules(), interpretive_reading(), rsi()
freq()):
+freq()):
speed improvement for microbial IDs
fixed factor level names for R Markdown
age_groups(), to let groups of fives and tens end with 100+ instead of 120+freq() for when all values are NA
+freq() for when all values are NA
first_isolate() for when dates are missingguess_ab_col()
@@ -1699,7 +1699,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
freq() function):
+freq() function):
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
@@ -1709,15 +1709,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # OLD WAY septic_patients %>% mutate(genus = mo_genus(mo)) %>% - freq(genus) + freq(genus) # NEW WAY septic_patients %>% - freq(mo_genus(mo)) + 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 to TRUE at default, even for markdown
Using portion_* functions now throws a warning when total available isolate is below argument minimum
Functions as.mo, as.rsi, as.mic, as.atc and freq will not set package name as attribute anymore
Frequency tables - freq():
Frequency tables - freq():
Support for grouping variables, test with:
@@ -1807,14 +1807,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
septic_patients %>%
group_by(hospital_id) %>%
- freq(gender)
+ freq(gender)
Support for (un)selecting columns:
Check for hms::is.hms
Removed diacritics from all authors (columns microorganisms$ref and microorganisms.old$ref) to comply with CRAN policy to only allow ASCII characters
Fix for mo_property not working properly
Fix for eucast_rules where some Streptococci would become ceftazidime R in EUCAST rule 4.5
Support for named vectors of class mo, useful for top_freq()
Support for named vectors of class mo, useful for top_freq()
ggplot_rsi and scale_y_percent have breaks argument
AI improvements for as.mo:
For lists, subsetting is possible:
my_list = list(age = septic_patients$age, gender = septic_patients$gender)
-my_list %>% freq(age)
-my_list %>% freq(gender)rsi (antimicrobial resistance) to use as inputtable to use as input: freq(table(x, y))
+table 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)
+freq(mydata, mycolumn) is the same as mydata %>% freq(mycolumn)
top_freq function to return the top/below n items as vectorA list in case of mo_taxonomy() and mo_info()
A named character in case of mo_url()
A numeric in case of mo_snomed()
A character with additional class taxonomic_name in case of mo_family(), mo_genus(), mo_name(), mo_fullname() and mo_shortname()
A character in all other cases
The Gram stain - mo_gramstain() - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, PMID 11837318), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value NA. Functions mo_is_gram_negative() and mo_is_gram_positive() always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria.
Determination of yeasts - mo_is_yeast() - will be based on the taxonomic kingdom and class. Budding yeasts are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). True yeasts are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return TRUE. It returns FALSE otherwise (except when the input is NA or the MO code is UNKNOWN).
Intrinsic resistance - mo_is_intrinsic_resistant() - will be determined based on the intrinsic_resistant data set, which is based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2 (2020). The mo_is_intrinsic_resistant() functions can be vectorised over arguments x (input for microorganisms) and over ab (input for antibiotics).
The functions mo_family(), mo_genus(), mo_name(), mo_fullname() and mo_shortname() are returned with an additional class taxonomic_name, which allows italic printing in tibbles and markdown tables such as with knitr::kable().
All output will be translated where possible.
The function mo_url() will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
SNOMED codes - mo_snomed() - are from the US Edition of SNOMED CT from 1 September 2020. See Source and the microorganisms data set for more info.