It cleanses existing data by providing new classes for microoganisms, antibiotics and antimicrobial results (both S/I/R and MIC). By installing this package, you teach R everything about microbiology that is needed for analysis. These functions all use intelligent rules to guess results that you would expect:
as.mo() to get a microbial ID. The IDs are human readable for the trained eye - the ID of Klebsiella pneumoniae is “B_KLBSL_PNE” (B stands for Bacteria) and the ID of S. aureus is “B_STPHY_AUR”. The function takes almost any text as input that looks like the name or code of a microorganism like “E. coli”, “esco” or “esccol” and tries to find expected results using intelligent rules combined with the included Catalogue of Life data set. It only takes milliseconds to find results, please see our benchmarks. Moreover, it can group Staphylococci into coagulase negative and positive (CoNS and CoPS, see source) and can categorise Streptococci into Lancefield groups (like beta-haemolytic Streptococcus Group B, source).as.ab() to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is AMX and the ID of gentamicin is GEN. The as.ab() function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, DDDs and categories of antibiotics. The function as.atc() will return the ATC code of an antibiotic as defined by the WHO.as.ab() to get an antibiotic ID. Like microbial IDs, these IDs are also human readable based on those used by EARS-Net. For example, the ID of amoxicillin is AMX and the ID of gentamicin is GEN. The as.ab() function also uses intelligent rules to find results like accepting misspelling, trade names and abbrevations used in many laboratory systems. For instance, the values “Furabid”, “Furadantin”, “nitro” all return the ID of Nitrofurantoine. To accomplish this, the package contains a database with most LIS codes, official names, trade names, DDDs and categories of antibiotics. The function as.atc() will return the ATC code of an antibiotic as defined by the WHO.as.rsi() to get antibiotic interpretations based on raw MIC values (in mg/L) or disk diffusion values (in mm), or transform existing values to valid antimicrobial results. It produces just S, I or R based on your input and warns about invalid values. Even values like “<=0.002; S” (combined MIC/RSI) will result in “S”.as.mic() to cleanse your MIC values. It produces a so-called factor (called ordinal in SPSS) with valid MIC values as levels. A value like “<=0.002; S” (combined MIC/RSI) will result in “<=0.002”.(no code changes yet)
+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() where misspelled input would not be understoodalso_single_tested parameter in count_* functionsFunction mo_synonyms() to get all previously accepted taxonomic names of a microorganism
count_df() and portion_df() are now lowercasemdr_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 recognisedeucast_rules() with verbose = TRUE
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_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()
-These functions use 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.
+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 tableas.atc()
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():
as.atc()
atc_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 versionsguess_atc() is now deprecated in favour of as.atc() and will be removed in future versionsas.mo():
as.mo(..., allow_uncertain = 3)Functions mo_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
as.mo(..., allow_uncertain = 3)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.:
ab_official("Bactroban")
+ab_official("Bactroban")
# [1] "Mupirocin"
ab_name(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"
@@ -976,7 +988,7 @@ Using as.mo(..., allow_uncertain = 3)
Function ratio to transform a vector of values to a preset ratio
-For example: ratio(c(10, 500, 10), ratio = "1:2:1") would return 130, 260, 130For example: ratio(c(10, 500, 10), ratio = "1:2:1") would return 130, 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
@@ -1002,9 +1014,9 @@ Using as.mo(..., allow_uncertain = 3)
-
+
-Changed
+Changed
- Improvements for forecasting with
resistance_predict and added more examples
- More antibiotics added as parameters for EUCAST rules
@@ -1034,7 +1046,7 @@ Using as.mo(..., allow_uncertain = 3)
- Now possible to coerce MIC values with a space between operator and value, i.e.
as.mic("<= 0.002") now works
- Classes
rsi and mic do not add the attribute package.version anymore
-- Added
"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.
+- Added
"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.
- Build-in host check for
atc_property as it requires the host set by url 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 the dplyr package v0.7.5 and above
@@ -1088,9 +1100,9 @@ Using as.mo(..., allow_uncertain = 3)New print format for tibbles and data.tables
-
+
-Changed
+Changed
- Fixed
rsi class for vectors that contain only invalid antimicrobial interpretations
- Renamed dataset
ablist to antibiotics
@@ -1147,7 +1159,7 @@ Using as.mo(..., allow_uncertain = 3)
Contents
@@ -241,21 +241,7 @@
- ratio(x, ratio)
-
-abname(...)
-
-atc_property(...)
-
-atc_official(...)
-
-ab_official(...)
-
-atc_name(...)
-
-atc_trivial_nl(...)
-
-atc_tradenames(...)
+ as.atc(x)
Read more on our website!
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html
index b0daef68..d9d01156 100644
--- a/docs/reference/WHONET.html
+++ b/docs/reference/WHONET.html
@@ -80,7 +80,7 @@
@@ -271,7 +271,7 @@
Inducible clindamycin resistanceClindamycin can be induced?
CommentOther comments
Date of data entryDate this data was entered in WHONET
AMP_ND10:CIP_EE27 different antibiotics. You can lookup the abbreviatons in the antibiotics data set, or use e.g. atc_name("AMP") to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using as.rsi.
AMP_ND10:CIP_EE27 different antibiotics. You can lookup the abbreviatons in the antibiotics data set, or use e.g. ab_name("AMP") to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using as.rsi.
Read more on our website!
diff --git a/docs/reference/count.html b/docs/reference/count.html
index 6b507f81..2b1f50a1 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of portion_S and R in case of portion_R). This would lead to selection bias in almost all cases.
a logical to indicate whether for combination therapies also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of portion_S and R in case of portion_R). This could lead to selection bias.
ggplot_rsi(data, position = NULL, x = "antibiotic", fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1), limits = NULL, translate_ab = "name", combine_SI = TRUE, - combine_IR = FALSE, language = get_locale(), fun = count_df, - nrow = NULL, colours = c(S = "#61a8ff", SI = "#61a8ff", I = - "#61f7ff", IR = "#ff6961", R = "#ff6961"), datalabels = TRUE, - datalabels.size = 2.5, datalabels.colour = "gray15", title = NULL, - subtitle = NULL, caption = NULL, x.title = NULL, y.title = NULL, - ...) + combine_IR = FALSE, language = get_locale(), nrow = NULL, + colours = c(S = "#61a8ff", SI = "#61a8ff", I = "#61f7ff", IR = + "#ff6961", R = "#ff6961"), datalabels = TRUE, datalabels.size = 2.5, + datalabels.colour = "gray15", title = NULL, subtitle = NULL, + caption = NULL, x.title = NULL, y.title = NULL, ...) geom_rsi(position = NULL, x = c("antibiotic", "interpretation"), fill = "interpretation", translate_ab = "name", language = get_locale(), combine_SI = TRUE, combine_IR = FALSE, - fun = count_df, ...) + ...) facet_rsi(facet = c("interpretation", "antibiotic"), nrow = NULL) @@ -316,10 +315,6 @@language language of the returned text, defaults to system language (see
get_locale) and can also be set withgetOption("AMR_locale"). Uselanguage = NULLorlanguage = ""to prevent translation.
function to transform data, either count_df (default) or portion_df
(when using facet) number of rows
show datalabels using labels_rsi_count, will only be shown when fun = count_df
show datalabels using labels_rsi_count
At default, the names of antibiotics will be shown on the plots using ab_name. This can be set with the translate_ab parameter. See count_df.
The functions
-geom_rsi will take any variable from the data that has an rsi class (created with as.rsi) using fun (count_df at default, can also be portion_df) and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
geom_rsi will take any variable from the data that has an rsi class (created with as.rsi) using rsi_df and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
facet_rsi creates 2d plots (at default based on S/I/R) using facet_wrap.
scale_y_percent transforms the y axis to a 0 to 100% range using scale_continuous.
scale_rsi_colours sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using scale_brewer.
Transform to antibiotic ID
Transform to ATC code
ratio() abname() atc_property() atc_official() ab_official() atc_name() atc_trivial_nl() atc_tradenames()
Deprecated functions
a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of portion_S and R in case of portion_R). This would lead to selection bias in almost all cases.
a logical to indicate whether for combination therapies also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of portion_S and R in case of portion_R). This could lead to selection bias.
gendergender of the patient
patient_idID of the patient, first 10 characters of an SHA hash containing irretrievable information
moID of microorganism created with as.mo, see also microorganisms
peni:rifa40 different antibiotics with class rsi (see as.rsi); these column names occur in antibiotics data set and can be translated with abname
peni:rifa40 different antibiotics with class rsi (see as.rsi); these column names occur in antibiotics data set and can be translated with ab_name