AMX for amoxicillinatc_certe, ab_umcg and atc_trivial_nl have been removedatc_* functions are superceded by ab_* functionsAll output will be translated by using an included, local translation file that can be found after install with:
- -Please create an issue in one of our repositories if you want additions in this file.ggplot_rsi():
@@ -297,19 +294,18 @@ Please create an issue in one of our repositories if you want additions in this
support for boxplots:
- +./inst/eucast/eucast.tsv
-age_groups(), to let groups of fives and tens end with 100+ instead of 120+StagedInstall: false to the DESCRIPTION fileNew 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()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()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 0.8.0as.atc()
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 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
as.atc()
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)# 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:
as.mo(..., allow_uncertain = 3)
-
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))
+# 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 to TRUE at default, even for markdown
@@ -625,10 +621,10 @@ Using as.mo(..., allow_uncertain = 3)Fewer than 3 characters as input for as.mo will return NA
-
Function as.mo (and all mo_* wrappers) now supports genus abbreviations with “species” attached
-
+
- Added parameter
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)
- Fix for
portion_*(..., as_percent = TRUE) when minimal number of isolates would not be met
@@ -641,15 +637,15 @@ Using as.mo(..., allow_uncertain = 3)
-
Support for grouping variables, test with:
-
+
-
Support for (un)selecting columns:
-
+
- Check for
hms::is.hms
@@ -729,18 +725,18 @@ Using as.mo(..., allow_uncertain = 3)
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"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"mo_gramstain("Esc blattae")
+# Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)
+# [1] "Gram negative"count_R, count_IR, count_I, count_SI and count_S to selectively count resistant or susceptible isolates
as.mo(..., allow_uncertain = 3)
-
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_GRA
+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:
-
+
- Added parameter
reference_df for as.mo, so users can supply their own microbial IDs, name or codes as a reference table
- Renamed all previous references to
bactid to mo, like:
@@ -790,12 +786,12 @@ Using as.mo(..., allow_uncertain = 3)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.:
-
+
- 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
@@ -806,13 +802,13 @@ Using as.mo(..., allow_uncertain = 3)
-
Support for quasiquotation in the functions series count_* and portions_*, and n_rsi. This allows to check for more than 2 vectors or columns.
-
+
- Edited
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.
- Fix for
ggplot_rsi when the ggplot2 package was not loaded
@@ -826,12 +822,12 @@ Using as.mo(..., allow_uncertain = 3)
-
Support for types (classes) list and matrix for freq
-
+
For lists, subsetting is possible:
-
+
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints", - "expert", "other", "all"), verbose = FALSE, ...) - -eucast_rules_file()+ "expert", "other", "all"), verbose = FALSE, ...)
| - + | EUCAST rules |