NEWS.md
- Speed improvement for eucast_rules()
Overall speed improvement by tweaking joining functions
Function mo_shortname() now return the genus for input where the species is unknown
BORSA is now recognised as an abbreviation for a Staphylococcus aureus, meaning that e.g. mo_genus("BORSA") will return “Staphylococcus”
Support for coloured tibble printing of classes mo, rsi, mic and disk
Making 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 parameter 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
support for boxplots:
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()
@@ -1266,7 +1270,7 @@ 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:
@@ -1275,15 +1279,15 @@ 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)) + freq(mo_genus(mo))Header info is now available as a list, with the header function
Using portion_* functions now throws a warning when total available isolate is below parameter minimum
Functions as.mo, as.rsi, as.mic, as.atc and freq will not set package name as attribute anymore
Frequency tables - freq():
Frequency tables - freq():
Support for grouping variables, test with:
Support for (un)selecting columns:
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 parameter
AI improvements for as.mo:
Support for types (classes) list and matrix for freq
my_matrix = with(septic_patients, matrix(c(age, gender), ncol = 2)) -freq(my_matrix) +freq(my_matrix)
For lists, subsetting is possible:
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 vectorTranslation table with 5,582 common microorganism codes
Translation table with 5,583 common microorganism codes
R/data.R
microorganisms.codes.RdA data.frame with 5,582 observations and 2 variables:
A data.frame with 5,583 observations and 2 variables:
code
Commonly used code of a microorganism
mo
ID of the microorganism in the microorganisms data set