Examples
-These rules can be used to discard impossible bug-drug combinations in your data. For example, Klebsiella produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of Klebsiella is resistant to ampicillin.
-Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, Klebsiella). EUCAST expert rules solve this, that can be applied using eucast_rules():
These rules can be used to discard impossible bug-drug combinations +in your data. For example, Klebsiella produces beta-lactamase +that prevents ampicillin (or amoxicillin) from working against it. In +other words, practically every strain of Klebsiella is +resistant to ampicillin.
+Sometimes, laboratory data can still contain such strains with
+ampicillin being susceptible to ampicillin. This could be because an
+antibiogram is available before an identification is available, and the
+antibiogram is then not re-interpreted based on the identification
+(namely, Klebsiella). EUCAST expert rules solve this, that can
+be applied using eucast_rules():
oops <- data.frame(mo = c("Klebsiella",
"Escherichia"),
@@ -226,7 +247,10 @@
# mo ampicillin
# 1 Klebsiella R
# 2 Escherichia SA more convenient function is mo_is_intrinsic_resistant() that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:
A more convenient function is
+mo_is_intrinsic_resistant() that uses the same guideline,
+but allows to check for one or more specific microorganisms or
+antibiotics:
mo_is_intrinsic_resistant(c("Klebsiella", "Escherichia"),
"ampicillin")
@@ -235,7 +259,11 @@
mo_is_intrinsic_resistant("Klebsiella",
c("ampicillin", "kanamycin"))
# [1] TRUE FALSEEUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called interpretive reading, is basically a form of imputation, and is part of the eucast_rules() function as well:
EUCAST rules can not only be used for correction, they can also be
+used for filling in known resistance and susceptibility based on results
+of other antimicrobials drugs. This process is called interpretive
+reading, is basically a form of imputation, and is part of the
+eucast_rules() function as well:
data <- data.frame(mo = c("Staphylococcus aureus",
"Enterococcus faecalis",
@@ -397,12 +425,14 @@
diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html
index e306389f..d6bd8507 100644
--- a/docs/articles/MDR.html
+++ b/docs/articles/MDR.html
@@ -44,7 +44,7 @@
How to determine multi-drug resistance (MDR)
+How to determine multi-drug resistance +(MDR)
Source:vignettes/MDR.Rmd
@@ -198,54 +199,87 @@
-With the function mdro(), you can determine which micro-organisms are multi-drug resistant organisms (MDRO).
With the function mdro(), you can determine which
+micro-organisms are multi-drug resistant organisms (MDRO).
Type of input
-The mdro() function takes a data set as input, such as a regular data.frame. It tries to automatically determine the right columns for info about your isolates, such as the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command ?mdro.
For WHONET data (and most other data), all settings are automatically set correctly.
+The mdro() function takes a data set as input, such as a
+regular data.frame. It tries to automatically determine the
+right columns for info about your isolates, such as the name of the
+species and all columns with results of antimicrobial agents. See the
+help page for more info about how to set the right settings for your
+data with the command ?mdro.
For WHONET data (and most other data), all settings are automatically +set correctly.
Guidelines
-The mdro() function support multiple guidelines. You can select a guideline with the guideline parameter. Currently supported guidelines are (case-insensitive):
The mdro() function support multiple guidelines. You can
+select a guideline with the guideline parameter. Currently
+supported guidelines are (case-insensitive):
-
-guideline = "CMI2012"(default)Magiorakos AP, Srinivasan A et al. “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (link)
+Magiorakos AP, Srinivasan A et al. “Multidrug-resistant, +extensively drug-resistant and pandrug-resistant bacteria: an +international expert proposal for interim standard definitions for +acquired resistance.” Clinical Microbiology and Infection (2012) (link)
-
-
-guideline = "EUCAST3.2"(or simplyguideline = "EUCAST")The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (link)
+
+guideline = "EUCAST3.2"(or simply +guideline = "EUCAST")The European international guideline - EUCAST Expert Rules Version +3.2 “Intrinsic Resistance and Unusual Phenotypes” (link)
-
-guideline = "EUCAST3.1"The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (link)
+The European international guideline - EUCAST Expert Rules Version +3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (link)
-
-guideline = "TB"The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (link)
+The international guideline for multi-drug resistant tuberculosis - +World Health Organization “Companion handbook to the WHO guidelines for +the programmatic management of drug-resistant tuberculosis” (link)
-
-guideline = "MRGN"The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6
+The German national guideline - Mueller et al. (2015) +Antimicrobial Resistance and Infection Control 4:7. DOI: +10.1186/s13756-015-0047-6
-
-guideline = "BRMO"The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (link)
+The Dutch national guideline - Rijksinstituut voor Volksgezondheid en +Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) +(ZKH)” (link)
Please suggest your own (country-specific) guidelines by letting us know: https://github.com/msberends/AMR/issues/new.
+Please suggest your own (country-specific) guidelines by letting us +know: https://github.com/msberends/AMR/issues/new.
Custom Guidelines
-You can also use your own custom guideline. Custom guidelines can be set with the custom_mdro_guideline() function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.
If you are familiar with case_when() of the dplyr package, you will recognise the input method to set your own rules. Rules must be set using what R considers to be the ‘formula notation’:
You can also use your own custom guideline. Custom guidelines can be
+set with the custom_mdro_guideline() function. This is of
+great importance if you have custom rules to determine MDROs in your
+hospital, e.g., rules that are dependent on ward, state of contact
+isolation or other variables in your data.
If you are familiar with case_when() of the
+dplyr package, you will recognise the input method to set
+your own rules. Rules must be set using what R considers to be the
+‘formula notation’:
custom <- custom_mdro_guideline(CIP == "R" & age > 60 ~ "Elderly Type A",
ERY == "R" & age > 60 ~ "Elderly Type B")If a row/an isolate matches the first rule, the value after the first ~ (in this case ‘Elderly Type A’) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.
You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.
+If a row/an isolate matches the first rule, the value after the first
+~ (in this case ‘Elderly Type A’) will be set as
+MDRO value. Otherwise, the second rule will be tried and so on. The
+maximum number of rules is unlimited.
You can print the rules set in the console for an overview. Colours +will help reading it if your console supports colours.
custom
# A set of custom MDRO rules:
@@ -255,7 +289,8 @@
#
# Unmatched rows will return NA.
# Results will be of class <factor>, with ordered levels: Negative < Elderly Type A < Elderly Type BThe outcome of the function can be used for the guideline argument in the mdro() function:
The outcome of the function can be used for the
+guideline argument in the mdro() function:
x <- mdro(example_isolates, guideline = custom)
# Determining MDROs based on custom rules, resulting in factor levels:
@@ -266,14 +301,25 @@
# x
# Negative Elderly Type A Elderly Type B
# 1070 198 732The rules set (the custom object in this case) could be exported to a shared file location using saveRDS() if you collaborate with multiple users. The custom rules set could then be imported using readRDS().
The rules set (the custom object in this case) could be
+exported to a shared file location using saveRDS() if you
+collaborate with multiple users. The custom rules set could then be
+imported using readRDS().
Examples
-The mdro() function always returns an ordered factor for predefined guidelines. For example, the output of the default guideline by Magiorakos et al. returns a factor with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.
The next example uses the example_isolates data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:
The mdro() function always returns an ordered
+factor for predefined guidelines. For example, the output
+of the default guideline by Magiorakos et al. returns a
+factor with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in
+that order.
The next example uses the example_isolates data set.
+This is a data set included with this package and contains full
+antibiograms of 2,000 microbial isolates. It reflects reality and can be
+used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline
+on this data set, we get:
Only results with ‘R’ are considered as resistance. Use combine_SI = FALSE to also consider ‘I’ as resistance.
Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x
+# Warning: in `mdro()`: NA introduced for isolates where the available percentage of +# antimicrobial classes was below 50% (set with `pct_required_classes`)Only results with ‘R’ are considered as resistance. Use
+combine_SI = FALSE to also consider ‘I’ as resistance.
Determining multidrug-resistant organisms (MDRO), according to: +Guideline: Multidrug-resistant, extensively drug-resistant and +pandrug-resistant bacteria: an international expert proposal for interim +standard definitions for acquired resistance. Author(s): Magiorakos AP, +Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: +Clinical Microbiology and Infection 18:3, 2012; doi: +10.1111/j.1469-0691.2011.03570.x
(16 isolates had no test results)
Frequency table
Class: factor > ordered (numeric)
Length: 2,000
-Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant …
+Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively
+drug-resistant …
Available: 1,729 (86.45%, NA: 271 = 13.55%)
Unique: 2
| Item | @@ -320,21 +382,22 @@ Unique: 21 | Negative | 1601 | -92.60% | +92.6% | 1601 | -92.60% | +92.6% | |
|---|---|---|---|---|---|---|---|---|---|
| 2 | Multi-drug-resistant (MDR) | 128 | -7.40% | +7.4% | 1729 | -100.00% | +100.0% |
For another example, I will create a data set to determine multi-drug resistant TB:
+For another example, I will create a data set to determine multi-drug +resistant TB:
# random_rsi() is a helper function to generate
# a random vector with values S, I and R
@@ -345,7 +408,8 @@ Unique: 2
pyrazinamide = random_rsi(5000),
moxifloxacin = random_rsi(5000),
kanamycin = random_rsi(5000))Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same way:
+Because all column names are automatically verified for valid drug +names or codes, this would have worked exactly the same way:
my_TB_data <- data.frame(RIF = random_rsi(5000),
INH = random_rsi(5000),
@@ -358,20 +422,21 @@ Unique: 2
head(my_TB_data)
# rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1 I R I S R S
-# 2 I S R R S R
-# 3 R I S I R S
-# 4 S S I R I S
-# 5 S R S S S I
-# 6 S R R S R I
+# 1 R S S I S I
+# 2 R S S S R I
+# 3 S S I I S S
+# 4 I I S S S S
+# 5 I R R I R R
+# 6 I R S I S S
# kanamycin
-# 1 S
-# 2 I
+# 1 I
+# 2 R
# 3 R
-# 4 R
+# 4 S
# 5 I
-# 6 R
-We can now add the interpretation of MDR-TB to our data set. You can use:
+# 6 IWe can now add the interpretation of MDR-TB to our data set. You can +use:
mdro(my_TB_data, guideline = "TB")or its shortcut mdr_tb():
Frequency table
Class: factor > ordered (numeric)
Length: 5,000
-Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <…
-Available: 5,000 (100.0%, NA: 0 = 0.0%)
+Levels: 5: Negative < Mono-resistant < Poly-resistant <
+Multi-drug-resistant <…
+Available: 5,000 (100%, NA: 0 = 0%)
Unique: 5
| Item | @@ -413,40 +487,40 @@ Unique: 5|||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 | Mono-resistant | -3250 | -65.00% | -3250 | -65.00% | +3175 | +63.50% | +3175 | +63.50% |
| 2 | Negative | -975 | -19.50% | -4225 | -84.50% | +1057 | +21.14% | +4232 | +84.64% |
| 3 | Multi-drug-resistant | -474 | -9.48% | -4699 | -93.98% | +431 | +8.62% | +4663 | +93.26% |
| 4 | Poly-resistant | -203 | -4.06% | -4902 | -98.04% | +236 | +4.72% | +4899 | +97.98% |
| 5 | Extensively drug-resistant | -98 | -1.96% | +101 | +2.02% | 5000 | 100.00% |
| Item | @@ -334,7 +361,7 @@ Longest: 40
|---|
(omitted 27 entries, n = 56 [11.20%])
+(omitted 27 entries, n = 56 [11.2%])
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
@@ -388,7 +415,8 @@ Drug group: Beta-lactams/penicillins
A first glimpse at results
-An easy ggplot will already give a lot of information, using the included ggplot_rsi() function:
+An easy ggplot will already give a lot of information,
+using the included ggplot_rsi() function:
data %>%
group_by(Country) %>%
@@ -408,12 +436,14 @@ Drug group: Beta-lactams/penicillins
diff --git a/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png
index 78144edc..0ce239d4 100644
Binary files a/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/WHONET_files/figure-html/unnamed-chunk-7-1.png differ
diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html
index 0e2362a8..7ca1bb22 100644
--- a/docs/articles/benchmarks.html
+++ b/docs/articles/benchmarks.html
@@ -44,7 +44,7 @@
@@ -198,14 +198,30 @@
-One of the most important features of this package is the complete microbial taxonomic database, supplied by the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). We created a function as.mo() that transforms any user input value to a valid microbial ID by using intelligent rules combined with the microbial taxonomy.
-Using the microbenchmark package, we can review the calculation performance of this function. Its function microbenchmark() runs different input expressions independently of each other and measures their time-to-result.
+One of the most important features of this package is the complete
+microbial taxonomic database, supplied by the Catalogue of Life (CoL) and
+the List of Prokaryotic names with
+Standing in Nomenclature (LPSN). We created a function
+as.mo() that transforms any user input value to a valid
+microbial ID by using intelligent rules combined with the microbial
+taxonomy.
+Using the microbenchmark package, we can review the
+calculation performance of this function. Its function
+microbenchmark() runs different input expressions
+independently of each other and measures their time-to-result.
-In the next test, we try to ‘coerce’ different input values into the microbial code of Staphylococcus aureus. Coercion is a computational process of forcing output based on an input. For microorganism names, coercing user input to taxonomically valid microorganism names is crucial to ensure correct interpretation and to enable grouping based on taxonomic properties.
-The actual result is the same every time: it returns its microorganism code B_STPHY_AURS (B stands for Bacteria, its taxonomic kingdom).
+In the next test, we try to ‘coerce’ different input values into the
+microbial code of Staphylococcus aureus. Coercion is a
+computational process of forcing output based on an input. For
+microorganism names, coercing user input to taxonomically valid
+microorganism names is crucial to ensure correct interpretation and to
+enable grouping based on taxonomic properties.
+The actual result is the same every time: it returns its
+microorganism code B_STPHY_AURS (B stands for
+Bacteria, its taxonomic kingdom).
But the calculation time differs a lot:
S.aureus <- microbenchmark(
@@ -224,27 +240,40 @@
times = 25)
print(S.aureus, unit = "ms", signif = 2)
# Unit: milliseconds
-# expr min lq mean median uq max neval
-# as.mo("sau") 10.0 12.0 20.0 12.0 15.0 53 25
-# as.mo("stau") 49.0 54.0 72.0 58.0 91.0 97 25
-# as.mo("STAU") 50.0 54.0 71.0 57.0 90.0 110 25
-# as.mo("staaur") 10.0 12.0 17.0 12.0 14.0 51 25
-# as.mo("STAAUR") 10.0 12.0 17.0 12.0 14.0 54 25
-# as.mo("S. aureus") 26.0 27.0 40.0 31.0 56.0 74 25
-# as.mo("S aureus") 26.0 27.0 39.0 29.0 58.0 68 25
-# as.mo("Staphylococcus aureus") 3.5 3.9 6.6 4.1 4.8 38 25
-# as.mo("Staphylococcus aureus (MRSA)") 230.0 240.0 250.0 240.0 250.0 280 25
-# as.mo("Sthafilokkockus aaureuz") 180.0 190.0 200.0 190.0 200.0 290 25
-# as.mo("MRSA") 11.0 12.0 19.0 13.0 14.0 50 25
-# as.mo("VISA") 21.0 22.0 32.0 25.0 50.0 60 25
+# expr min lq mean median uq max neval
+# as.mo("sau") 12.0 13 18.0 14.0 15.0 48 25
+# as.mo("stau") 54.0 59 80.0 91.0 96.0 99 25
+# as.mo("STAU") 53.0 61 77.0 66.0 94.0 100 25
+# as.mo("staaur") 12.0 13 19.0 14.0 16.0 62 25
+# as.mo("STAAUR") 12.0 13 16.0 14.0 15.0 48 25
+# as.mo("S. aureus") 28.0 30 38.0 33.0 35.0 69 25
+# as.mo("S aureus") 27.0 31 46.0 34.0 65.0 73 25
+# as.mo("Staphylococcus aureus") 3.7 4 6.7 4.3 4.5 36 25
+# as.mo("Staphylococcus aureus (MRSA)") 260.0 270 290.0 280.0 290.0 360 25
+# as.mo("Sthafilokkockus aaureuz") 190.0 210 220.0 210.0 220.0 330 25
+# as.mo("MRSA") 12.0 13 20.0 14.0 16.0 68 25
+# as.mo("VISA") 22.0 23 32.0 25.0 27.0 63 25
-In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 200 milliseconds, this is only 5 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations are up to 47 times slower to determine.
-To improve performance, we implemented two important algorithms to save unnecessary calculations: repetitive results and already precalculated results.
+In the table above, all measurements are shown in milliseconds
+(thousands of seconds). A value of 5 milliseconds means it can determine
+200 input values per second. It case of 200 milliseconds, this is only 5
+input values per second. It is clear that accepted taxonomic names are
+extremely fast, but some variations are up to 67 times slower to
+determine.
+To improve performance, we implemented two important algorithms to
+save unnecessary calculations: repetitive results and
+already precalculated results.
Repetitive results
-Repetitive results are values that are present more than once in a vector. Unique values will only be calculated once by as.mo(). So running as.mo(c("E. coli", "E. coli")) will check the value "E. coli" only once.
-To prove this, we will use mo_name() for testing - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses as.mo() internally.
+Repetitive results are values that are present more than once in a
+vector. Unique values will only be calculated once by
+as.mo(). So running
+as.mo(c("E. coli", "E. coli")) will check the value
+"E. coli" only once.
+To prove this, we will use mo_name() for testing - a
+helper function that returns the full microbial name (genus, species and
+possibly subspecies) which uses as.mo() internally.
# start with the example_isolates data set
x <- example_isolates %>%
@@ -258,8 +287,8 @@
# what do these values look like? They are of class <mo>:
head(x)
# Class <mo>
-# [1] B_STPHY_AURS B_STRPT_EQNS B_KLBSL_PNMN B_STPHY_EPDR B_STPHY_AURS
-# [6] B_CRYNB_STRT
+# [1] B_ESCHR_COLI B_STRPT_MITS B_STRPT_ANGN B_STPHY_CONS B_ESCHR_COLI
+# [6] B_ESCHR_COLI
# as the example_isolates data set has 2,000 rows, we should have 2 million items
length(x)
@@ -275,13 +304,20 @@
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# mo_name(x) 196 209 274 223 364 388 10
-So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.223 seconds. That is 112 nanoseconds on average. You only lose time on your unique input values.
+# mo_name(x) 207 225 288 233 370 414 10
+So getting official taxonomic names of 2,000,000 (!!) items
+consisting of 90 unique values only takes 0.233 seconds. That is 117
+nanoseconds on average. You only lose time on your unique input
+values.
Precalculated results
-What about precalculated results? If the input is an already precalculated result of a helper function such as mo_name(), it almost doesn’t take any time at all. In other words, if you run mo_name() on a valid taxonomic name, it will return the results immediately (see ‘C’ below):
What about precalculated results? If the input is an already
+precalculated result of a helper function such as
+mo_name(), it almost doesn’t take any time at all. In other
+words, if you run mo_name() on a valid taxonomic name, it
+will return the results immediately (see ‘C’ below):
run_it <- microbenchmark(A = mo_name("STAAUR"),
B = mo_name("S. aureus"),
@@ -289,11 +325,14 @@
times = 10)
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
-# expr min lq mean median uq max neval
-# A 8.00 9.16 9.19 9.28 9.46 9.73 10
-# B 23.40 27.20 32.60 27.90 28.10 80.20 10
-# C 1.85 2.25 2.40 2.47 2.62 2.90 10So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0025 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:
So going from mo_name("Staphylococcus aureus") to
+"Staphylococcus aureus" takes 0.0028 seconds - it doesn’t
+even start calculating if the result would be the same as the
+expected resulting value. That goes for all helper functions:
run_it <- microbenchmark(A = mo_species("aureus"),
B = mo_genus("Staphylococcus"),
@@ -307,20 +346,28 @@
print(run_it, unit = "ms", signif = 3)
# Unit: milliseconds
# expr min lq mean median uq max neval
-# A 1.76 1.80 2.07 1.95 2.26 2.90 10
-# B 1.69 1.73 1.90 1.81 2.03 2.48 10
-# C 1.71 1.77 1.92 1.91 2.05 2.17 10
-# D 1.68 1.71 1.76 1.76 1.82 1.88 10
-# E 1.68 1.70 1.89 1.89 2.04 2.26 10
-# F 1.67 1.75 1.93 1.89 2.11 2.35 10
-# G 1.70 1.76 1.97 1.88 2.12 2.43 10
-# H 1.67 1.71 1.83 1.75 1.98 2.14 10Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" anyway, there is no point in calculating the result. And because this package contains all phyla of all known bacteria, it can just return the initial value immediately.
Of course, when running mo_phylum("Firmicutes") the
+function has zero knowledge about the actual microorganism, namely
+S. aureus. But since the result would be
+"Firmicutes" anyway, there is no point in calculating the
+result. And because this package contains all phyla of all known
+bacteria, it can just return the initial value immediately.
Results in other languages
-When the system language is non-English and supported by this AMR package, some functions will have a translated result. This almost does’t take extra time (compare “en” from the table below with the other languages):
When the system language is non-English and supported by this
+AMR package, some functions will have a translated result.
+This almost does’t take extra time (compare “en” from the table below
+with the other languages):
CoNS <- as.mo("CoNS")
CoNS
@@ -349,18 +396,19 @@
times = 100)
print(run_it, unit = "ms", signif = 4)
# Unit: milliseconds
-# expr min lq mean median uq max neval
-# da 1.9470 2.0220 2.190 2.0720 2.358 3.234 100
-# de 1.9560 2.0330 3.649 2.1610 2.401 50.670 100
-# en 0.8937 0.9124 1.022 0.9776 1.120 1.748 100
-# es 1.9710 2.0290 2.216 2.1000 2.391 3.109 100
-# fr 1.8280 1.8960 3.214 1.9420 2.237 71.550 100
-# it 1.9370 1.9970 2.163 2.0610 2.339 3.210 100
-# nl 1.9710 2.0280 2.698 2.1110 2.421 49.340 100
-# pt 1.8920 1.9600 2.119 2.0200 2.261 3.265 100
-# ru 1.8630 1.9420 2.779 2.0270 2.335 66.660 100
-# sv 1.8680 1.9190 4.062 1.9890 2.263 78.870 100Currently supported languages are Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish.
+# expr min lq mean median uq max neval +# da 2.1730 2.476 3.956 2.609 2.873 45.180 100 +# de 2.2170 2.497 3.161 2.646 2.855 48.260 100 +# en 0.9509 1.122 1.640 1.183 1.321 38.430 100 +# es 2.1870 2.546 2.763 2.659 2.872 5.676 100 +# fr 1.9880 2.339 2.609 2.456 2.636 5.197 100 +# it 2.2580 2.475 4.081 2.619 2.867 47.080 100 +# nl 2.3120 2.535 2.792 2.664 2.822 8.113 100 +# pt 2.1930 2.417 3.329 2.528 2.783 48.600 100 +# ru 2.0470 2.360 2.596 2.481 2.683 6.030 100 +# sv 2.2030 2.443 3.077 2.545 2.703 43.350 100Currently supported languages are Danish, Dutch, English, French, +German, Italian, Portuguese, Russian, Spanish and Swedish.
Data sets for download / own use
-10 March 2022
+14 March 2022
Source:vignettes/datasets.Rmd
datasets.RmdNeeded R packages
-As with many uses in R, we need some additional packages for AMR data analysis. Our package works closely together with the tidyverse packages dplyr and ggplot2 by Dr Hadley Wickham. The tidyverse tremendously improves the way we conduct data science - it allows for a very natural way of writing syntaxes and creating beautiful plots in R.
Our AMR package depends on these packages and even extends their use and functions.
As with many uses in R, we need some additional packages for AMR data
+analysis. Our package works closely together with the tidyverse packages dplyr and ggplot2 by Dr
+Hadley Wickham. The tidyverse tremendously improves the way we conduct
+data science - it allows for a very natural way of writing syntaxes and
+creating beautiful plots in R.
Our AMR package depends on these packages and even
+extends their use and functions.
library(dplyr)
library(ggplot2)
-library(AMR)
+library(AMR)
# (if not yet installed, install with:)
# install.packages(c("tidyverse", "AMR"))Prediction analysis
-Our package contains a function resistance_predict(), which takes the same input as functions for other AMR data analysis. Based on a date column, it calculates cases per year and uses a regression model to predict antimicrobial resistance.
Our package contains a function resistance_predict(),
+which takes the same input as functions for other
+AMR data analysis. Based on a date column, it calculates cases per
+year and uses a regression model to predict antimicrobial
+resistance.
It is basically as easy as:
# resistance prediction of piperacillin/tazobactam (TZP):
resistance_predict(tbl = example_isolates, col_date = "date", col_ab = "TZP", model = "binomial")
@@ -228,10 +237,16 @@
predict_TZP <- example_isolates %>%
resistance_predict(col_ab = "TZP",
model = "binomial")The function will look for a date column itself if col_date is not set.
When running any of these commands, a summary of the regression model will be printed unless using resistance_predict(..., info = FALSE).
The function will look for a date column itself if
+col_date is not set.
When running any of these commands, a summary of the regression model
+will be printed unless using
+resistance_predict(..., info = FALSE).
# ℹ Using column 'date' as input for `col_date`.This text is only a printed summary - the actual result (output) of the function is a data.frame containing for each year: the number of observations, the actual observed resistance, the estimated resistance and the standard error below and above the estimation:
This text is only a printed summary - the actual result (output) of
+the function is a data.frame containing for each year: the
+number of observations, the actual observed resistance, the estimated
+resistance and the standard error below and above the estimation:
predict_TZP
# year value se_min se_max observations observed estimated
@@ -264,13 +279,20 @@
# 27 2028 0.43730688 0.3418075 0.5328063 NA NA 0.43730688
# 28 2029 0.46175755 0.3597639 0.5637512 NA NA 0.46175755
# 29 2030 0.48639359 0.3782932 0.5944939 NA NA 0.48639359
-# 30 2031 0.51109592 0.3973697 0.6248221 NA NA 0.51109592The function plot is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:
The function plot is available in base R, and can be
+extended by other packages to depend the output based on the type of
+input. We extended its function to cope with resistance predictions:
plot(predict_TZP)
This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.
-We also support the ggplot2 package with our custom function ggplot_rsi_predict() to create more appealing plots:
This is the fastest way to plot the result. It automatically adds the +right axes, error bars, titles, number of available observations and +type of model.
+We also support the ggplot2 package with our custom
+function ggplot_rsi_predict() to create more appealing
+plots:
ggplot_rsi_predict(predict_TZP)
Choosing the right model
-Resistance is not easily predicted; if we look at vancomycin resistance in Gram-positive bacteria, the spread (i.e. standard error) is enormous:
+Resistance is not easily predicted; if we look at vancomycin +resistance in Gram-positive bacteria, the spread (i.e. standard error) +is enormous:
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
@@ -290,8 +314,13 @@
ggplot_rsi_predict()
# ℹ Using column 'date' as input for `col_date`.
Vancomycin resistance could be 100% in ten years, but might also stay around 0%.
-You can define the model with the model parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.
Vancomycin resistance could be 100% in ten years, but might also stay +around 0%.
+You can define the model with the model parameter. The
+model chosen above is a generalised linear regression model using a
+binomial distribution, assuming that a period of zero resistance was
+followed by a period of increasing resistance leading slowly to more and
+more resistance.
Valid values are:
-"binomial" or "binom" or "logit"
+"binomial" or "binom" or
+"logit"
|
glm(..., family = binomial) |
Generalised linear model with binomial distribution | @@ -328,7 +358,9 @@
For the vancomycin resistance in Gram-positive bacteria, a linear model might be more appropriate since no binomial distribution is to be expected based on the observed years:
+For the vancomycin resistance in Gram-positive bacteria, a linear +model might be more appropriate since no binomial distribution is to be +expected based on the observed years:
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
@@ -337,7 +369,8 @@
# ℹ Using column 'date' as input for `col_date`.
This seems more likely, doesn’t it?
-The model itself is also available from the object, as an attribute:
The model itself is also available from the object, as an
+attribute:
model <- attributes(predict_TZP)$model
@@ -366,12 +399,14 @@
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diff --git a/docs/articles/welcome_to_AMR.html b/docs/articles/welcome_to_AMR.html
index 5539d3ba..9a1ac845 100644
--- a/docs/articles/welcome_to_AMR.html
+++ b/docs/articles/welcome_to_AMR.html
@@ -44,7 +44,7 @@
Note: to keep the package size as small as possible, we only included this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDRO’s, find explanation of EUCAST rules, and much more: https://msberends.github.io/AMR/articles/.
+Note: to keep the package size as small as possible, we only included +this vignette on CRAN. You can read more vignettes on our website about +how to conduct AMR data analysis, determine MDRO’s, find explanation of +EUCAST rules, and much more: https://msberends.github.io/AMR/articles/.
-
AMR is a free, open-source and independent R package (see Copyright) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
-The AMR package is available in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.
+AMR is a free, open-source and independent R package
+(see Copyright)
+to simplify the analysis and prediction of Antimicrobial Resistance
+(AMR) and to work with microbial and antimicrobial data and properties,
+by using evidence-based methods. Our aim is to provide a
+standard for clean and reproducible antimicrobial resistance
+data analysis, that can therefore empower epidemiological analyses to
+continuously enable surveillance and treatment evaluation in any
+setting.
After installing this package, R knows ~71,000 distinct microbial +species and all ~570 antibiotic, antimycotic and antiviral drugs by name +and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and +knows all about valid R/SI and MIC values. It supports any data format, +including WHONET/EARS-Net data.
+The AMR package is available in Danish, Dutch, English,
+French, German, Italian, Portuguese, Russian, Spanish and Swedish.
+Antimicrobial drug (group) names and colloquial microorganism names are
+provided in these languages.
This package is fully independent of any other R package and works on +Windows, macOS and Linux with all versions of R since R-3.0 (April +2013). It was designed to work in any setting, including those +with very limited resources. Since its first public release in +early 2018, this package has been downloaded from more than 175 +countries.
This package can be used for:
-
-
- Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature -
- Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines -
- Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records +
- Reference for the taxonomy of microorganisms, since the package +contains all microbial (sub)species from the Catalogue of Life and List +of Prokaryotic names with Standing in Nomenclature +
- Interpreting raw MIC and disk diffusion values, based on the latest +CLSI or EUCAST guidelines +
- Retrieving antimicrobial drug names, doses and forms of +administration from clinical health care records
- Determining first isolates to be used for AMR data analysis
- Calculating antimicrobial resistance -
- Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) -
- Calculating (empirical) susceptibility of both mono therapy and combination therapies -
- Predicting future antimicrobial resistance using regression models -
- Getting properties for any microorganism (like Gram stain, species, genus or family) -
- Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) +
- Determining multi-drug resistance (MDR) / multi-drug resistant +organisms (MDRO) +
- Calculating (empirical) susceptibility of both mono therapy and +combination therapies +
- Predicting future antimicrobial resistance using regression +models +
- Getting properties for any microorganism (like Gram stain, species, +genus or family) +
- Getting properties for any antibiotic (like name, code of +EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name)
- Plotting antimicrobial resistance
- Applying EUCAST expert rules -
- Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code -
- Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code -
- Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI +
- Getting SNOMED codes of a microorganism, or getting properties of a +microorganism based on a SNOMED code +
- Getting LOINC codes of an antibiotic, or getting properties of an +antibiotic based on a LOINC code +
- Machine reading the EUCAST and CLSI guidelines from 2011-2020 to +translate MIC values and disk diffusion diameters to R/SI
- Principal component analysis for AMR
All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this AMR package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find all download links on our website, which is automatically updated with every code change.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375) but is actively and durably maintained (see changelog)) by two public healthcare organisations in the Netherlands.
+All reference data sets (about microorganisms, antibiotics, R/SI
+interpretation, EUCAST rules, etc.) in this AMR package are
+publicly and freely available. We continually export our data sets to
+formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
+files that are machine-readable and suitable for input in any software
+program, such as laboratory information systems. Please find all
+download links on our website, which is automatically updated with
+every code change.
This R package was created for both routine data analysis and +academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration +with non-profit organisations Certe +Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This +R package formed the basis of two PhD theses (DOI +10.33612/diss.177417131 and DOI +10.33612/diss.192486375) but is actively and durably maintained (see +changelog)) +by two public healthcare organisations in the Netherlands.
-AMR 1.8.0.9004
-Last updated: 3 March 2022
-All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
+
+AMR 1.8.1
+All functions in this package are considered to be stable. Updates to +the AMR interpretation rules (such as by EUCAST and CLSI), the microbial +taxonomy, and the antibiotic dosages will all be updated every 6 to 12 +months.
Changed
-Support for antibiotic interpretations of the MIPS laboratory system:
"U"for S (‘susceptible urine’),"D"for I (‘susceptible dose-dependent’)
+Fix for using
as.rsi()on values containing capped +values (such as>=), sometimes leading to +NA
+Support for antibiotic interpretations of the MIPS laboratory +system:
"U"for S (‘susceptible urine’),"D"+for I (‘susceptible dose-dependent’)-
-
Improved algorithm of
+as.mo(), especially for ignoring non-taxonomic text, such as:Improved algorithm of
as.mo(), especially for +ignoring non-taxonomic text, such as:-mo_name("methicillin-resistant S. aureus (MRSA)") @@ -177,113 +184,220 @@Updated MIC printing in tibbles
Changed
+
AMR 1.8.02022-01-07
Breaking changes
-- Removed
p_symbol()and allfilter_*()functions (except forfilter_first_isolate()), which were all deprecated in a previous package version
- - Removed the
key_antibiotics()andkey_antibiotics_equal()functions, which were deprecated and superseded bykey_antimicrobials()andantimicrobials_equal()+- Removed
p_symbol()and allfilter_*()+functions (except forfilter_first_isolate()), which were +all deprecated in a previous package version
+ - Removed the
key_antibiotics()and +key_antibiotics_equal()functions, which were deprecated +and superseded bykey_antimicrobials()and +antimicrobials_equal()
- - Removed all previously implemented
ggplot2::ggplot()generics for classes<mic>,<disk>,<rsi>and<resistance_predict>as they did not follow theggplot2logic. They were replaced withggplot2::autoplot()generics.
- - Renamed function
get_locale()toget_AMR_locale()to prevent conflicts with other packages
+ - Removed all previously implemented
ggplot2::ggplot()+generics for classes<mic>, +<disk>,<rsi>and +<resistance_predict>as they did not follow the +ggplot2logic. They were replaced with +ggplot2::autoplot()generics.
+ - Renamed function
get_locale()to +get_AMR_locale()to prevent conflicts with other +packages
- Removed
New
-Support for the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the
rsi_translationdata set. This data set now more strictly follows the WHONET software as well.
-Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for
eucast_rules(),mo_is_intrinsic_resistant()andmdro(). Theintrinsic_resistantdata set was also updated accordingly.
-Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
+Support for the CLSI 2021 guideline for interpreting MIC/disk +diffusion values, which are incorporated in the +
rsi_translationdata set. This data set now more strictly +follows the WHONET software as well.
+Support for EUCAST Intrinsic Resistance and Unusual Phenotypes +v3.3 (October 2021). This is now the default EUCAST guideline in the +package (all older guidelines are still available) for +
eucast_rules(),mo_is_intrinsic_resistant()+andmdro(). Theintrinsic_resistantdata set +was also updated accordingly.
+Support for all antimicrobial drug (group) names and colloquial +microorganism names in Danish, Dutch, English, French, German, Italian, +Portuguese, Russian, Spanish and Swedish
-
-
Function
+set_ab_names()to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc. Its second argument can be a tidyverse way of selecting:Function
set_ab_names()to rename data set columns +that resemble antimicrobial drugs. This allows for quickly renaming +columns to official names, ATC codes, etc. Its second argument can be a +tidyverse way of selecting:example_isolates %>% set_ab_names(where(is.rsi)) example_isolates %>% set_ab_names(AMC:GEN, property = "atc") - -
Function
ab_ddd_units()to get units of DDDs (daily defined doses), deprecating the use ofab_ddd(..., units = TRUE)to be more consistent in data types of function output
+Function
ab_ddd_units()to get units of DDDs (daily +defined doses), deprecating the use of +ab_ddd(..., units = TRUE)to be more consistent in data +types of function output
Changed
-- Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new staphylococcal species named since 1 January last year -
- The
antibioticsdata set now contains all ATC codes that are available through the WHOCC website, regardless of drugs being present in more than one ATC group. This means that: -- Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5) +
- Updated the bacterial taxonomy to 5 October 2021 (according to LPSN), including all 11 new +staphylococcal species named since 1 January last year +
- The
antibioticsdata set now contains all ATC +codes that are available through the WHOCC website, regardless of drugs being +present in more than one ATC group. This means that: +- Some drugs now contain multiple ATC codes (e.g., metronidazole +contains 5)
-
-
antibiotics$atcis now alistcontainingcharactervectors, and thisatccolumn was moved to the 5th position of theantibioticsdata set
+
antibiotics$atcis now alistcontaining +charactervectors, and thisatccolumn was +moved to the 5th position of theantibioticsdata set -
-
ab_atc()does not always return a character vector of length 1, and returns alistif the input is larger than length 1
+
ab_atc()does not always return a character vector of +length 1, and returns alistif the input is larger than +length 1 -
ab_info()has a slightly different output
- - Some DDDs (daily defined doses) were added or updated according to newly included ATC codes +
- Some DDDs (daily defined doses) were added or updated according to +newly included ATC codes
They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package
-Added more selectors for antibiotic classes:
aminopenicillins(),antifungals(),antimycobacterials(),lincosamides(),lipoglycopeptides(),polymyxins(),quinolones(),streptogramins(),trimethoprims()andureidopenicillins()
+They now also work in R-3.0 and R-3.1, supporting every version +of R since 2013 like the rest of the package
+Added more selectors for antibiotic classes: +
aminopenicillins(),antifungals(), +antimycobacterials(),lincosamides(), +lipoglycopeptides(),polymyxins(), +quinolones(),streptogramins(), +trimethoprims()and +ureidopenicillins()-
-
Added specific selectors for certain types for treatment:
+administrable_per_os()andadministrable_iv(), which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):Added specific selectors for certain types for treatment: +
administrable_per_os()andadministrable_iv(), +which are based on available Defined Daily Doses (DDDs), as defined by +the WHOCC. These are ideal for e.g. analysing pathogens in primary care +where IV treatment is not an option. They can be combined with other AB +selectors, e.g. to select penicillins that are only administrable per os +(i.e., orally):example_isolates[, penicillins() & administrable_per_os()] # base R example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr -
-
Added the selector
+ab_selector(), which accepts a filter to be used internally on theantibioticsdata set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:Added the selector
ab_selector(), which accepts a +filter to be used internally on theantibioticsdata set, +yielding great flexibility on drug properties, such as selecting +antibiotic columns with an oral DDD of at least 1 gram:example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")] # base R example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr
- Added the selector
not_intrinsic_resistant(), which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of E. coli and K. pneumoniae and contains a column “vancomycin”, this column will be removed (or rather, unselected) using this function.
-Added argument
only_treatable, which defaults toTRUEand will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
-Fix for using selectors multiple times in one call (e.g., using them in
dplyr::filter()and immediately after indplyr::select())
-Fix for using having multiple columns that are coerced to the same antibiotic agent
-Fixed for using
all()orany()on antibiotic selectors in an R Markdown file
+Added the selector
not_intrinsic_resistant(), which +only keeps antibiotic columns that are not intrinsic resistant for all +microorganisms in a data set, based on the latest EUCAST guideline on +intrinsic resistance. For example, if a data set contains only +microorganism codes or names of E. coli and K. +pneumoniae and contains a column “vancomycin”, this column will be +removed (or rather, unselected) using this function.
+Added argument
only_treatable, which defaults to +TRUEand will exclude drugs that are only for laboratory +tests and not for treating patients (such as imipenem/EDTA and +gentamicin-high)
+Fix for using selectors multiple times in one call (e.g., using +them in
dplyr::filter()and immediately after in +dplyr::select())
+Fix for using having multiple columns that are coerced to the +same antibiotic agent
+Fixed for using
all()orany()on +antibiotic selectors in an R Markdown file
mo_gramstain()) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as Negativicoccus and Veillonella.mo_gramstain()) determination of
+the taxonomic class Negativicutes within the phylum of Firmicutes - they
+were considered Gram-positives because of their phylum but are actually
+Gram-negative. This impacts 137 taxonomic species, genera and families,
+such as Negativicoccus and Veillonella.first_isolate()
NAs for old MO codes when running as.mo() on themproportion_*() and count_*() functions failas.mo()
+NAs for old MO codes when
+running as.mo() on themproportion_*() and count_*() functions
+failas.mo()
col_* arguments are left blank, e.g. in first_isolate()
+col_* arguments
+are left blank, e.g. in first_isolate()
random_mic(), random_disk() and random_rsi() are now enforcedrandom_mic(),
+random_disk() and random_rsi() are now
+enforcedas.rsi() has an improved algorithm and can now also correct for textual input (such as “Susceptible”, “Resistant”) in all supported languagesas.rsi() has an improved algorithm and can now also
+correct for textual input (such as “Susceptible”, “Resistant”) in all
+supported languages
as.mic() has an improved algorithmcount_*(), proportion_*() function (or resistant() or susceptible()), the dplyr group will be shown, if availablescale_rsi_colours() when using ggplot2 v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)count_*(), proportion_*() function (or
+resistant() or susceptible()), the
+dplyr group will be shown, if availablescale_rsi_colours() when
+using ggplot2 v3.3.4 or higher (this is ggplot2 bug 4511,
+soon to be fixed)as.mo()
random_mic()
+random_mic()
as.ab() and all ab_*() functionsfortify() extensions for plotting methodsas.ab() and all ab_*()
+functionsfortify() extensions for plotting methodsNA values of the classes <mic>, <disk> and <rsi> are now exported objects of this package, e.g. NA_mic_ is an NA of class mic (just like the base R NA_character_ is an NA of class character)proportion_df(), count_df() and rsi_df() functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packagesmdro() function now returns NA for all rows that have no test resultsspecies_id column in the microorganisms data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and mo_url() has been updated to reflect this change.get_episode() and is_new_episode()
+NA values of the classes <mic>,
+<disk> and <rsi> are now exported
+objects of this package, e.g. NA_mic_ is an NA
+of class mic (just like the base R
+NA_character_ is an NA of class
+character)proportion_df(), count_df() and
+rsi_df() functions now return with the additional S3 class
+‘rsi_df’ so they can be extended by other packagesmdro() function now returns NA for all
+rows that have no test resultsspecies_id column in the
+microorganisms data set now only contains LPSN record
+numbers. For this reason, this column is now numeric instead of a
+character, and mo_url() has been updated to reflect this
+change.get_episode() and
+is_new_episode()
get_episode() and is_new_episode() can now cope with NAsget_episode() and is_new_episode() can now
+cope with NAs
Breaking change
-
-
All antibiotic class selectors (such as
+carbapenems(),aminoglycosides()) can now be used for filtering as well, making all their accompanyingfilter_*()functions redundant (such asfilter_carbapenems(),filter_aminoglycosides()). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:All antibiotic class selectors (such as +
carbapenems(),aminoglycosides()) can now be +used for filtering as well, making all their accompanying +filter_*()functions redundant (such as +filter_carbapenems(), +filter_aminoglycosides()). These functions are now +deprecated and will be removed in a next release. Examples of how the +selectors can be used for filtering:# select columns with results for carbapenems @@ -312,71 +433,144 @@New
-- Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using
as.rsi())
- - Function
custom_eucast_rules()that brings support for custom AMR rules ineucast_rules()+- Support for CLSI 2020 guideline for interpreting MICs and disk
+diffusion values (using
as.rsi())
+ - Function
custom_eucast_rules()that brings support for +custom AMR rules ineucast_rules()
- - Function
italicise_taxonomy()to make taxonomic names within a string italic, with support for markdown and ANSI
- - Support for all four methods to determine first isolates as summarised by Hindler et al. (doi: 10.1086/511864): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
-
- The
first_isolate()function gained the argumentmethodthat has to be “phenotype-based”, “episode-based”, “patient-based”, or “isolate-based”. The old behaviour is equal to “episode-based”. The new default is “phenotype-based” if antimicrobial test results are available, and “episode-based” otherwise. This new default will yield slightly more isolates for selection (which is a good thing).
- - Since fungal isolates can also be selected, the functions
key_antibiotics()andkey_antibiotics_equal()are now deprecated in favour of thekey_antimicrobials()andantimicrobials_equal()functions. Also, the newall_antimicrobials()function works like the oldkey_antibiotics()function, but includes any column with antimicrobial test results. Usingkey_antimicrobials()still only selects six preferred antibiotics for Gram-negatives, six for Gram-positives, and six universal antibiotics. It has a newantifungalargument to set antifungal agents (antimycotics).
- - Using
type == "points"in thefirst_isolate()function for phenotype-based selection will now consider all antimicrobial drugs in the data set, using the newall_antimicrobials()+ - Function
italicise_taxonomy()to make taxonomic names +within a string italic, with support for markdown and ANSI
+ - Support for all four methods to determine first isolates as
+summarised by Hindler et al. (doi: 10.1086/511864):
+isolate-based, patient-based, episode-based and phenotype-based. The
+last method is now the default.
+
- The
first_isolate()function gained the argument +methodthat has to be “phenotype-based”, “episode-based”, +“patient-based”, or “isolate-based”. The old behaviour is equal to +“episode-based”. The new default is “phenotype-based” if antimicrobial +test results are available, and “episode-based” otherwise. This new +default will yield slightly more isolates for selection (which is a good +thing).
+ - Since fungal isolates can also be selected, the functions
+
key_antibiotics()andkey_antibiotics_equal()+are now deprecated in favour of thekey_antimicrobials()+andantimicrobials_equal()functions. Also, the new +all_antimicrobials()function works like the old +key_antibiotics()function, but includes any column with +antimicrobial test results. Usingkey_antimicrobials()+still only selects six preferred antibiotics for Gram-negatives, six for +Gram-positives, and six universal antibiotics. It has a new +antifungalargument to set antifungal agents +(antimycotics).
+ - Using
type == "points"in the +first_isolate()function for phenotype-based selection will +now consider all antimicrobial drugs in the data set, using the new +all_antimicrobials()
- - The
first_isolate()function can now take a vector of values forcol_keyantibioticsand can have an episode length ofInf+ - The
first_isolate()function can now take a vector of +values forcol_keyantibioticsand can have an episode +length ofInf
- - Since the phenotype-based method is the new default,
filter_first_isolate()renders thefilter_first_weighted_isolate()function redundant. For this reason,filter_first_weighted_isolate()is now deprecated.
- - The documentation of the
first_isolate()andkey_antimicrobials()functions has been completely rewritten.
+ - Since the phenotype-based method is the new default,
+
filter_first_isolate()renders the +filter_first_weighted_isolate()function redundant. For +this reason,filter_first_weighted_isolate()is now +deprecated.
+ - The documentation of the
first_isolate()and +key_antimicrobials()functions has been completely +rewritten.
- - The
- Function
betalactams()as additional antbiotic column selector and functionfilter_betalactams()as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
- - A
ggplot()method forresistance_predict()+ - Function
betalactams()as additional antbiotic column +selector and functionfilter_betalactams()as additional +antbiotic column filter. The group of betalactams consists of all +carbapenems, cephalosporins and penicillins.
+ - A
ggplot()method for +resistance_predict()
- The
- Support for CLSI 2020 guideline for interpreting MICs and disk
+diffusion values (using
Changed
-
-
bug_drug_combinations()now supports grouping using thedplyrpackage
- - Custom MDRO guidelines (
mdro(),custom_mdro_guideline()): -- Custom MDRO guidelines can now be combined with other custom MDRO guidelines using
c()+bug_drug_combinations()now supports grouping using the +dplyrpackage
+ - Custom MDRO guidelines (
mdro(), +custom_mdro_guideline()): +- Custom MDRO guidelines can now be combined with other custom MDRO
+guidelines using
c()
- - Fix for applying the rules; in previous versions, rows were interpreted according to the last matched rule. Now, rows are interpreted according to the first matched rule +
- Fix for applying the rules; in previous versions, rows were +interpreted according to the last matched rule. Now, rows are +interpreted according to the first matched rule
- Custom MDRO guidelines can now be combined with other custom MDRO
+guidelines using
- Fix for
age_groups()for persons aged zero
- - The
example_isolatesdata set now contains some (fictitious) zero-year old patients
+ - The
example_isolatesdata set now contains some +(fictitious) zero-year old patients - Fix for minor translation errors -
- Printing of microbial codes in a
data.frameortibblenow gives a warning if the data contains old microbial codes (from a previous AMR package version)
+ - Printing of microbial codes in a
data.frameor +tibblenow gives a warning if the data contains old +microbial codes (from a previous AMR package version) - Extended the
like()functions: -Now checks if
patternis a valid regular expression
+Now checks if
patternis a valid regular +expression-
-
Added
+%unlike%and%unlike_case%(as negations of the existing%like%and%like_case%). This greatly improves readability:Added
%unlike%and%unlike_case%(as +negations of the existing%like%and +%like_case%). This greatly improves readability:
- Altered the RStudio addin, so it now iterates over
%like%->%unlike%->%like_case%->%unlike_case%if you keep pressing your keyboard shortcut
+Altered the RStudio addin, so it now iterates over +
%like%->%unlike%-> +%like_case%->%unlike_case%if you keep +pressing your keyboard shortcut
- Fixed an installation error on R-3.0 -
- Added
infoargument toas.mo()to turn on/off the progress bar
- - Fixed a bug where
col_moin some functions (esp.eucast_rules()andmdro()) could not be a column name of themicroorganismsdata set as it would throw an error
- - Fix for transforming numeric values to RSI (
as.rsi()) when thevctrspackage is loaded (i.e., when using tidyverse)
+ - Added
infoargument toas.mo()to turn +on/off the progress bar
+ - Fixed a bug where
col_moin some functions +(esp.eucast_rules()andmdro()) could not be +a column name of themicroorganismsdata set as it would +throw an error
+ - Fix for transforming numeric values to RSI (
as.rsi()) +when thevctrspackage is loaded (i.e., when using +tidyverse) - Colour fix for using
barplot()on an RSI class
- - Added 25 common system codes for bacteria to the
microorganisms.codesdata set
- - Added 16 common system codes for antimicrobial agents to the
antibioticsdata set
- - Fix for using
skimr::skim()on classesmo,micanddiskwhen using the just releaseddplyrv1.0.6
- - Updated
skimr::skim()usage for MIC values to also include 25th and 75th percentiles
+ - Added 25 common system codes for bacteria to the
+
microorganisms.codesdata set
+ - Added 16 common system codes for antimicrobial agents to the
+
antibioticsdata set
+ - Fix for using
skimr::skim()on classesmo, +micanddiskwhen using the just released +dplyrv1.0.6
+ - Updated
skimr::skim()usage for MIC values to also +include 25th and 75th percentiles - Fix for plotting missing MIC/disk diffusion values -
- Updated join functions to always use
dplyrjoin functions if thedplyrpackage is installed - now also preserving grouped variables
- - Antibiotic class selectors (such as
cephalosporins()) now maintain the column order from the original data
+ - Updated join functions to always use
dplyrjoin +functions if thedplyrpackage is installed - now also +preserving grouped variables
+ - Antibiotic class selectors (such as
cephalosporins()) +now maintain the column order from the original data - Fix for selecting columns using
fluoroquinolones() -
-
age()now vectorises over bothxandreference+age()now vectorises over bothxand +reference
- Custom MDRO guidelines can now be combined with other custom MDRO guidelines using
Other
-- As requested by CRAN administrators: decreased package size by 3 MB in costs of a slower loading time of the package -
- All unit tests are now processed by the
tinytestpackage, instead of thetestthatpackage. Thetestthatpackage unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, thetinytestpackage is very lightweight and dependency-free.
+ - As requested by CRAN administrators: decreased package size by 3 MB +in costs of a slower loading time of the package +
- All unit tests are now processed by the
tinytest+package, instead of thetestthatpackage. The +testthatpackage unfortunately requires tons of +dependencies that are also heavy and only usable for recent R versions, +disallowing developers to test a package under any R 3.* version. On the +contrary, thetinytestpackage is very lightweight and +dependency-free.
- Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using
New
-
-
Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the
-eucast_rules()function and inas.rsi()to interpret MIC and disk diffusion values. This is now the default guideline in this package.- Added function
eucast_dosage()to get adata.framewith advised dosages of a certain bug-drug combination, which is based on the newdosagedata set
- - Added data set
dosageto fuel the neweucast_dosage()function and to make this data available in a structured way
- - Existing data set
example_isolatesnow reflects the latest EUCAST rules
+ - Added function
eucast_dosage()to get a +data.framewith advised dosages of a certain bug-drug +combination, which is based on the newdosagedata set
+ - Added data set
dosageto fuel the new +eucast_dosage()function and to make this data available in +a structured way
+ - Existing data set
example_isolatesnow reflects the +latest EUCAST rules
Support for EUCAST Clinical Breakpoints v11.0 (2021), effective +in the
+eucast_rules()function and inas.rsi()+to interpret MIC and disk diffusion values. This is now the default +guideline in this package. - Added function
-
-
Added argument
-only_rsi_columnsfor some functions, which defaults toFALSE, to indicate if the functions must only be applied to columns that are of class<rsi>(i.e., transformed withas.rsi()). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:- All antibiotic selector functions (
ab_class()and its wrappers, such asaminoglycosides(),carbapenems(),penicillins())
- - All antibiotic filter functions (
filter_ab_class()and its wrappers, such asfilter_aminoglycosides(),filter_carbapenems(),filter_penicillins())
+ - All antibiotic selector functions (
ab_class()and its +wrappers, such asaminoglycosides(), +carbapenems(),penicillins())
+ - All antibiotic filter functions (
filter_ab_class()and +its wrappers, such asfilter_aminoglycosides(), +filter_carbapenems(), +filter_penicillins()) eucast_rules()-
-
mdro()(including wrappers such asbrmo(),mrgn()andeucast_exceptional_phenotypes())
+
Added argument
+only_rsi_columnsfor some functions, +which defaults toFALSE, to indicate if the functions must +only be applied to columns that are of class<rsi>+(i.e., transformed withas.rsi()). This increases speed +since automatic determination of antibiotic columns is not needed +anymore. Affected functions are:mdro()(including wrappers such asbrmo(), +mrgn()and +eucast_exceptional_phenotypes()) - All antibiotic selector functions (
guess_ab_col()
Functions oxazolidinones() (an antibiotic selector function) and filter_oxazolidinones() (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
Functions oxazolidinones() (an antibiotic selector
+function) and filter_oxazolidinones() (an antibiotic filter
+function) to select/filter on e.g. linezolid and tedizolid
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>
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>
Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:
Function mo_is_yeast(), which determines whether a
+microorganism is a member of the taxonomic class Saccharomycetes or the
+taxonomic order Saccharomycetales:
mo_kingdom(c("Aspergillus", "Candida"))
@@ -424,7 +645,8 @@
# usage for filtering data:
example_isolates[which(mo_is_yeast()), ] # base R
example_isolates %>% filter(mo_is_yeast()) # dplyrThe mo_type() function has also been updated to reflect this change:
The mo_type() function has also been updated to reflect
+this change:
Added Pretomanid (PMD, J04AK08) to the antibiotics data set
Added Pretomanid (PMD, J04AK08) to the antibiotics
+data set
MIC values (see as.mic()) can now be used in any mathematical processing, such as usage inside functions min(), max(), range(), and with binary operators (+, -, etc.). This allows for easy distribution analysis and fast filtering on MIC values:
MIC values (see as.mic()) can now be used in any
+mathematical processing, such as usage inside functions
+min(), max(), range(), and with
+binary operators (+, -, etc.). This allows for
+easy distribution analysis and fast filtering on MIC values:
x <- random_mic(10)
@@ -453,49 +680,107 @@
Changed
- Updated the bacterial taxonomy to 3 March 2021 (using LPSN)
-
- Added 3,372 new species and 1,523 existing species became synomyms
-- The URL of a bacterial species (
mo_url()) will now lead to https://lpsn.dsmz.de
+- Added 3,372 new species and 1,523 existing species became
+synomyms
+- The URL of a bacterial species (
mo_url()) will now lead
+to https://lpsn.dsmz.de
-- Big update for plotting classes
rsi, <mic>, and <disk>:
-- Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
-- All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
-- Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see
translate)
-- Plotting is now possible with base R using
plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
+- Big update for plotting classes
rsi,
+<mic>, and <disk>:
+- Plotting of MIC and disk diffusion values now support interpretation
+colouring if you supply the microorganism and antimicrobial agent
+- All colours were updated to colour-blind friendly versions for
+values R, S and I for all plot methods (also applies to tibble
+printing)
+- Interpretation of MIC and disk diffusion values to R/SI will now be
+translated if the system language is German, Dutch or Spanish (see
+
translate)
+- Plotting is now possible with base R using
plot() and
+with ggplot2 using ggplot() on any vector of MIC and disk
+diffusion values
-- Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the
microorganisms data set
+- Updated SNOMED codes to US Edition of SNOMED CT from 1 September
+2020 and added the source to the help page of the
+
microorganisms data set
-
-
is.rsi() and is.rsi.eligible() now return a vector of TRUE/FALSE when the input is a data set, by iterating over all columns
-- Using functions without setting a data set (e.g.,
mo_is_gram_negative(), mo_is_gram_positive(), mo_is_intrinsic_resistant(), first_isolate(), mdro()) now work with dplyrs group_by() again
+is.rsi() and is.rsi.eligible() now return
+a vector of TRUE/FALSE when the input is a
+data set, by iterating over all columns
+- Using functions without setting a data set (e.g.,
+
mo_is_gram_negative(), mo_is_gram_positive(),
+mo_is_intrinsic_resistant(), first_isolate(),
+mdro()) now work with dplyrs
+group_by() again
-
-
first_isolate() can be used with group_by() (also when using a dot . as input for the data) and now returns the names of the groups
-- Updated the data set
microorganisms.codes (which contains popular LIS and WHONET codes for microorganisms) for some species of Mycobacterium that previously incorrectly returned M. africanum
+first_isolate() can be used with
+group_by() (also when using a dot . as input
+for the data) and now returns the names of the groups
+- Updated the data set
microorganisms.codes (which
+contains popular LIS and WHONET codes for microorganisms) for some
+species of Mycobacterium that previously incorrectly returned
+M. africanum
-- WHONET code
"PNV" will now correctly be interpreted as PHN, the antibiotic code for phenoxymethylpenicillin (‘peni V’)
-- Fix for verbose output of
mdro(..., verbose = TRUE) for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only P. aeruginosa)
+- WHONET code
"PNV" will now correctly be interpreted as
+PHN, the antibiotic code for phenoxymethylpenicillin (‘peni
+V’)
+- Fix for verbose output of
mdro(..., verbose = TRUE) for
+German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only
+P. aeruginosa)
-
-
is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
-- Functions
get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)
-- Argument
ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
-- Functions
print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
+is.rsi.eligible() now detects if the column name
+resembles an antibiotic name or code and now returns TRUE
+immediately if the input contains any of the values “R”, “S” or “I”.
+This drastically improves speed, also for a lot of other functions that
+rely on automatic determination of antibiotic columns.
+- Functions
get_episode() and
+is_new_episode() now support less than a day as value for
+argument episode_days (e.g., to include one patient/test
+per hour)
+- Argument
ampc_cephalosporin_resistance in
+eucast_rules() now also applies to value “I” (not only
+“S”)
+- Functions
print() and summary() on a
+Principal Components Analysis object (pca()) now print
+additional group info if the original data was grouped using
+dplyr::group_by()
-- Improved speed and reliability of
guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.
-- Fix for
mo_name() when used in other languages than English
-- The
like() function (and its fast alias %like%) now always use Perl compatibility, improving speed for many functions in this package (e.g., as.mo() is now up to 4 times faster)
+- Improved speed and reliability of
guess_ab_col(). As
+this also internally improves the reliability of
+first_isolate() and mdro(), this might have a
+slight impact on the results of those functions.
+- Fix for
mo_name() when used in other languages than
+English
+- The
like() function (and its fast alias
+%like%) now always use Perl compatibility, improving speed
+for many functions in this package (e.g., as.mo() is now up
+to 4 times faster)
-
-Staphylococcus cornubiensis is now correctly categorised as coagulase-positive
+Staphylococcus cornubiensis is now correctly categorised as
+coagulase-positive
-
-
random_disk() and random_mic() now have an expanded range in their randomisation
-- Support for GISA (glycopeptide-intermediate S. aureus), so e.g.
mo_genus("GISA") will return "Staphylococcus"
+random_disk() and random_mic() now have an
+expanded range in their randomisation
+- Support for GISA (glycopeptide-intermediate S. aureus), so
+e.g.
mo_genus("GISA") will return
+"Staphylococcus"
-- Added translations of German and Spanish for more than 200 antimicrobial drugs
-- Speed improvement for
as.ab() when the input is an official name or ATC code
-- Added argument
include_untested_rsi to the first_isolate() functions (defaults to TRUE to keep existing behaviour), to be able to exclude rows where all R/SI values (class <rsi>, see as.rsi()) are empty
+- Added translations of German and Spanish for more than 200
+antimicrobial drugs
+- Speed improvement for
as.ab() when the input is an
+official name or ATC code
+- Added argument
include_untested_rsi to the
+first_isolate() functions (defaults to TRUE to
+keep existing behaviour), to be able to exclude rows where all R/SI
+values (class <rsi>, see as.rsi()) are
+empty
Other
- Big documentation updates
-- Loading the package (i.e.,
library(AMR)) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
+- Loading the package (i.e.,
library(AMR)) now is ~50
+times faster than before, in costs of package size (which increased by
+~3 MB)
New
-
-
Functions
+get_episode()andis_new_episode()to determine (patient) episodes which are not necessarily based on microorganisms. Theget_episode()function returns the index number of the episode per group, while theis_new_episode()function returns valuesTRUE/FALSEto indicate whether an item in a vector is the start of a new episode. They also supportdplyrs grouping (i.e. usinggroup_by()):Functions
get_episode()and +is_new_episode()to determine (patient) episodes which are +not necessarily based on microorganisms. Theget_episode()+function returns the index number of the episode per group, while the +is_new_episode()function returns values +TRUE/FALSEto indicate whether an item in a +vector is the start of a new episode. They also support +dplyrs grouping (i.e. usinggroup_by()):
- Functions
mo_is_gram_negative()andmo_is_gram_positive()as wrappers aroundmo_gramstain(). They always returnTRUEorFALSE(except when the input isNAor the MO code isUNKNOWN), thus always returnFALSEfor species outside the taxonomic kingdom of Bacteria.
-Function
mo_is_intrinsic_resistant()to test for intrinsic resistance, based on EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
-Functions
random_mic(),random_disk()andrandom_rsi()for random value generation. The functionsrandom_mic()andrandom_disk()take microorganism names and antibiotic names as input to make generation more realistic.
+Functions
mo_is_gram_negative()and +mo_is_gram_positive()as wrappers around +mo_gramstain(). They always returnTRUEor +FALSE(except when the input isNAor the MO +code isUNKNOWN), thus always returnFALSEfor +species outside the taxonomic kingdom of Bacteria.
+Function
mo_is_intrinsic_resistant()to test for +intrinsic resistance, based on EUCAST +Intrinsic Resistance and Unusual Phenotypes v3.2 from 2020.
+Functions
random_mic(),random_disk()+andrandom_rsi()for random value generation. The functions +random_mic()andrandom_disk()take +microorganism names and antibiotic names as input to make generation +more realistic.
Changed
-New argument
ampc_cephalosporin_resistanceineucast_rules()to correct for AmpC de-repressed cephalosporin-resistant mutants
+New argument
ampc_cephalosporin_resistancein +eucast_rules()to correct for AmpC de-repressed +cephalosporin-resistant mutants-
-
Interpretation of antimicrobial resistance -
-as.rsi():- Reference data used for
as.rsi()can now be set by the user, using thereference_dataargument. This allows for using own interpretation guidelines. The user-set data must have the same structure asrsi_translation.
- - Better determination of disk zones and MIC values when running
as.rsi()on a data.frame
- - Fix for using
as.rsi()on a data.frame in older R versions
+ - Reference data used for
as.rsi()can now be set by the +user, using thereference_dataargument. This allows for +using own interpretation guidelines. The user-set data must have the +same structure asrsi_translation.
+ - Better determination of disk zones and MIC values when running
+
as.rsi()on a data.frame
+ - Fix for using
as.rsi()on a data.frame in older R +versions -
-
as.rsi()on a data.frame will not print a message anymore if the values are already clean R/SI values
- - If using
as.rsi()on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this
- - Fix for using
as.rsi()on adata.framethat only contains one column for antibiotic interpretations
+
Interpretation of antimicrobial resistance - +
+as.rsi():as.rsi()on a data.frame will not print a message +anymore if the values are already clean R/SI values
+ - Reference data used for
- If using
as.rsi()on MICs or disk diffusion while there +is intrinsic antimicrobial resistance, a warning will be thrown to +remind about this
+ - Fix for using
as.rsi()on adata.frame+that only contains one column for antibiotic interpretations -
-
Some functions are now context-aware when used inside
+dplyrverbs, such asfilter(),mutate()andsummarise(). This means that then the data argument does not need to be set anymore. This is the case for the new functions:Some functions are now context-aware when used inside +
dplyrverbs, such asfilter(), +mutate()andsummarise(). This means that then +the data argument does not need to be set anymore. This is the case for +the new functions:mo_is_gram_negative()mo_is_gram_positive()mo_is_intrinsic_resistant()
@@ -560,36 +879,72 @@
as_tibble()
For antibiotic selection functions (such as cephalosporins(), aminoglycosides()) to select columns based on a certain antibiotic group, the dependency on the tidyselect package was removed, meaning that they can now also be used without the need to have this package installed and now also work in base R function calls (they rely on R 3.2 or later):
For antibiotic selection functions (such as
+cephalosporins(), aminoglycosides()) to select
+columns based on a certain antibiotic group, the dependency on the
+tidyselect package was removed, meaning that they can now
+also be used without the need to have this package installed and now
+also work in base R function calls (they rely on R 3.2 or later):
# above example in base R:
example_isolates[which(first_isolate() & mo_is_gram_negative()),
c("mo", cephalosporins(), aminoglycosides())]For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the typed package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.
Fix for set_mo_source(), that previously would not remember the file location of the original file
Deprecated function p_symbol() that not really fits the scope of this package. It will be removed in a future version. See here for the source code to preserve it.
Updated coagulase-negative staphylococci determination with Becker et al. 2020 (PMID 32056452), meaning that the species S. argensis, S. caeli, S. debuckii, S. edaphicus and S. pseudoxylosus are now all considered CoNS
Fix for using argument reference_df in as.mo() and mo_*() functions that contain old microbial codes (from previous package versions)
Fixed a bug where mo_uncertainties() would not return the results based on the MO matching score
Fixed a bug where as.mo() would not return results for known laboratory codes for microorganisms
Fixed a bug where as.ab() would sometimes fail
For all function arguments in the code, it is now defined what
+the exact type of user input should be (inspired by the typed
+package). If the user input for a certain function does not meet the
+requirements for a specific argument (such as the class or length), an
+informative error will be thrown. This makes the package more robust and
+the use of it more reproducible and reliable. In total, more than 420
+arguments were defined.
Fix for set_mo_source(), that previously would not
+remember the file location of the original file
Deprecated function p_symbol() that not really fits
+the scope of this package. It will be removed in a future version. See
+here
+for the source code to preserve it.
Updated coagulase-negative staphylococci determination with +Becker et al. 2020 (PMID 32056452), meaning that the species +S. argensis, S. caeli, S. debuckii, S. +edaphicus and S. pseudoxylosus are now all considered +CoNS
Fix for using argument reference_df in
+as.mo() and mo_*() functions that contain old
+microbial codes (from previous package versions)
Fixed a bug where mo_uncertainties() would not
+return the results based on the MO matching score
Fixed a bug where as.mo() would not return results
+for known laboratory codes for microorganisms
Fixed a bug where as.ab() would sometimes
+fail
Better tibble printing for MIC values
Fix for plotting MIC values with plot()
Added plot() generic to class <disk>
LA-MRSA and CA-MRSA are now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g. mo_genus("LA-MRSA") will return "Staphylococcus" and mo_is_gram_positive("LA-MRSA") will return TRUE.
Fix for printing class NA
Fix for mo_shortname() when the input contains NA
If as.mo() takes more than 30 seconds, some suggestions will be done to improve speed
Added plot() generic to class
+<disk>
LA-MRSA and CA-MRSA are now recognised as an abbreviation for
+Staphylococcus aureus, meaning that
+e.g. mo_genus("LA-MRSA") will return
+"Staphylococcus" and
+mo_is_gram_positive("LA-MRSA") will return
+TRUE.
Fix for printing class NA
Fix for mo_shortname() when the input contains
+NA
If as.mo() takes more than 30 seconds, some
+suggestions will be done to improve speed
Other
-- All messages and warnings thrown by this package now break sentences on whole words +
- All messages and warnings thrown by this package now break sentences +on whole words
- More extensive unit tests -
- Internal calls to
options()were all removed in favour of a new internal environmentpkg_env+ - Internal calls to
options()were all removed in favour +of a new internal environmentpkg_env
- - Improved internal type setting (among other things: replaced all
sapply()calls withvapply())
+ - Improved internal type setting (among other things: replaced all
+
sapply()calls withvapply()) - Added CodeFactor as a continuous code review to this package: https://www.codefactor.io/repository/github/msberends/amr/
- Added Dr. Rogier Schade as contributor @@ -599,11 +954,31 @@
Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the
eucast_rules()function can now correct for more than 180 different antibiotics and themdro()function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. Theeucast_rules()function consequently gained the argumentsversion_breakpoints(at the moment defaults to v10.0, 2020) andversion_expertrules(at the moment defaults to v3.2, 2020). Theexample_isolatesdata set now also reflects the change from v3.1 to v3.2. Themdro()function now acceptsguideline == "EUCAST3.1"andguideline == "EUCAST3.2".
-A new vignette and website page with info about all our public and freely available data sets, that can be downloaded as flat files or in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
+Support for ‘EUCAST Expert Rules’ / ‘EUCAST Intrinsic Resistance +and Unusual Phenotypes’ version 3.2 of May 2020. With this addition to +the previously implemented version 3.1 of 2016, the +
eucast_rules()function can now correct for more than 180 +different antibiotics and themdro()function can determine +multidrug resistance based on more than 150 different antibiotics. All +previously implemented versions of the EUCAST rules are now maintained +and kept available in this package. Theeucast_rules()+function consequently gained the arguments +version_breakpoints(at the moment defaults to v10.0, 2020) +andversion_expertrules(at the moment defaults to v3.2, +2020). Theexample_isolatesdata set now also reflects the +change from v3.1 to v3.2. Themdro()function now accepts +guideline == "EUCAST3.1"and +guideline == "EUCAST3.2".
+A new vignette and website page with info about all our public +and freely available data sets, that can be downloaded as flat files or +in formats for use in R, SPSS, SAS, Stata and Excel: https://msberends.github.io/AMR/articles/datasets.html
-
-
Data set
-intrinsic_resistant. This data set contains all bug-drug combinations where the ‘bug’ is intrinsic resistant to the ‘drug’ according to the latest EUCAST insights. It contains just two columns:microorganismandantibiotic.Curious about which enterococci are actually intrinsic resistant to vancomycin?
+Data set
+intrinsic_resistant. This data set contains +all bug-drug combinations where the ‘bug’ is intrinsic resistant to the +‘drug’ according to the latest EUCAST insights. It contains just two +columns:microorganismandantibiotic.Curious about which enterococci are actually intrinsic resistant to +vancomycin?
Support for veterinary ATC codes
-Support for skimming classes
<rsi>,<mic>,<disk>and<mo>with theskimrpackage
+Support for skimming classes
<rsi>, +<mic>,<disk>and +<mo>with theskimrpackageAlthough advertised that this package should work under R 3.0.0, we still had a dependency on R 3.6.0. This is fixed, meaning that our package should now work under R 3.0.0.
+Although advertised that this package should work under R 3.0.0, +we still had a dependency on R 3.6.0. This is fixed, meaning that our +package should now work under R 3.0.0.
-
Improvements for
as.rsi():-
-
Support for using
+dplyr’sacross()to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.Support for using
dplyr’sacross()to +interpret MIC values or disk zone diameters, which also automatically +determines the column with microorganism names or codes.
- Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g.
as.rsi(df, col1:col9)
-Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.
-Added argument ‘add_intrinsic_resistance’ (defaults to
FALSE), that considers intrinsic resistance according to EUCAST
-Fixed a bug where in EUCAST rules the breakpoint for R would be interpreted as “>=” while this should have been “<”
+Cleaning columns in a data.frame now allows you to specify those +columns with tidy selection, +e.g.
as.rsi(df, col1:col9)
+Big speed improvement for interpreting MIC values and disk zone +diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 +values in total), our benchmarks showed a total run time going from +80.7-85.1 seconds to 1.8-2.0 seconds.
+Added argument ‘add_intrinsic_resistance’ (defaults to +
FALSE), that considers intrinsic resistance according to +EUCAST
+Fixed a bug where in EUCAST rules the breakpoint for R would be +interpreted as “>=” while this should have been “<”
-
-
-
-
Added intelligent data cleaning to
+as.disk(), so numbers can also be extracted from text and decimal numbers will always be rounded up:Added intelligent data cleaning to
as.disk(), so +numbers can also be extracted from text and decimal numbers will always +be rounded up:as.disk(c("disk zone: 23.4 mm", 23.4)) @@ -648,47 +1039,102 @@Improvements for
-as.mo():- A completely new matching score for ambiguous user input, using
mo_matching_score(). Any user input value that could mean more than one taxonomic entry is now considered ‘uncertain’. Instead of a warning, a message will be thrown and the accompanyingmo_uncertainties()has been changed completely; it now prints all possible candidates with their matching score.
- - Big speed improvement for already valid microorganism ID. This also means an significant speed improvement for using
mo_*functions likemo_name()on microoganism IDs.
- - Added argument
ignore_patterntoas.mo()which can also be given tomo_*functions likemo_name(), to exclude known non-relevant input from analysing. This can also be set with the optionAMR_ignore_pattern.
+ - A completely new matching score for ambiguous user input, using
+
mo_matching_score(). Any user input value that could mean +more than one taxonomic entry is now considered ‘uncertain’. Instead of +a warning, a message will be thrown and the accompanying +mo_uncertainties()has been changed completely; it now +prints all possible candidates with their matching score.
+ - Big speed improvement for already valid microorganism ID. This also
+means an significant speed improvement for using
mo_*+functions likemo_name()on microoganism IDs.
+ - Added argument
ignore_patterntoas.mo()+which can also be given tomo_*functions like +mo_name(), to exclude known non-relevant input from +analysing. This can also be set with the option +AMR_ignore_pattern.
get_locale()now uses at defaultSys.getenv("LANG")or, ifLANGis not set,Sys.getlocale(). This can be overwritten by setting the optionAMR_locale.get_locale()now uses at default +Sys.getenv("LANG")or, ifLANGis not set, +Sys.getlocale(). This can be overwritten by setting the +optionAMR_locale.Big speed improvement for
eucast_rules()Overall speed improvement by tweaking joining functions
Function
mo_shortname()now returns the genus for input where the species is unknownBORSA is now recognised as an abbreviation for Staphylococcus aureus, meaning that e.g.
mo_genus("BORSA")will return “Staphylococcus”Added a feature from AMR 1.1.0 and earlier again, but now without other package dependencies:
tibbleprinting support for classes<rsi>,<mic>,<disk>,<ab>and<mo>. When usingtibbles containing antimicrobial columns (class<rsi>), “S” will print in green, “I” will print in yellow and “R” will print in red. Microbial IDs (class<mo>) will emphasise on the genus and species, not on the kingdom.Names of antiviral agents in data set
antiviralsnow have a starting capital letter, like it is the case in theantibioticsdata setUpdated the documentation of the
WHONETdata set to clarify that all patient names are fictitiousFunction
mo_shortname()now returns the genus for +input where the species is unknownBORSA is now recognised as an abbreviation for Staphylococcus +aureus, meaning that e.g.
mo_genus("BORSA")will +return “Staphylococcus”Added a feature from AMR 1.1.0 and earlier again, but now without +other package dependencies:
tibbleprinting support for +classes<rsi>,<mic>, +<disk>,<ab>and +<mo>. When usingtibbles containing +antimicrobial columns (class<rsi>), “S” will print +in green, “I” will print in yellow and “R” will print in red. Microbial +IDs (class<mo>) will emphasise on the genus and +species, not on the kingdom.Names of antiviral agents in data set
antiviralsnow +have a starting capital letter, like it is the case in the +antibioticsdata setUpdated the documentation of the
WHONETdata set to +clarify that all patient names are fictitiousSmall
as.ab()algorithm improvementsFix for combining MIC values with raw numbers, i.e.
c(as.mic(2), 2)previously failed but now returns a valid MIC classggplot_rsi()andgeom_rsi()gained argumentsminimumandlanguage, to influence the internal use ofrsi_df()Fix for combining MIC values with raw numbers, +i.e.
c(as.mic(2), 2)previously failed but now returns a +valid MIC classggplot_rsi()andgeom_rsi()gained +argumentsminimumandlanguage, to influence +the internal use ofrsi_df()Changes in the
antibioticsdata set:- Updated oral and parental DDDs from the WHOCC
- Added abbreviation “piptazo” to ‘Piperacillin/tazobactam’ (TZP) -
- ‘Penicillin G’ (for intravenous use) is now named ‘Benzylpenicillin’ (code
PEN)
- - ‘Penicillin V’ (for oral use, code
PNV) was removed, since its actual entry ‘Phenoxymethylpenicillin’ (codePHN) already existed
- - The group name (
antibiotics$group) of ‘Linezolid’ (LNZ), ‘Cycloserine’ (CYC), ‘Tedizolid’ (TZD) and ‘Thiacetazone’ (THA) is now “Oxazolidinones” instead of “Other antibacterials”
+ - ‘Penicillin G’ (for intravenous use) is now named ‘Benzylpenicillin’
+(code
PEN)
+ - ‘Penicillin V’ (for oral use, code
PNV) was removed, +since its actual entry ‘Phenoxymethylpenicillin’ (codePHN) +already existed
+ - The group name (
antibiotics$group) of ‘Linezolid’ +(LNZ), ‘Cycloserine’ (CYC), ‘Tedizolid’ +(TZD) and ‘Thiacetazone’ (THA) is now +“Oxazolidinones” instead of “Other antibacterials”
Added support for using
unique()on classes<rsi>,<mic>,<disk>,<ab>and<mo>Added argument
excessto thekurtosis()function (defaults toFALSE), to return the excess kurtosis, defined as the kurtosis minus three.Added support for using
unique()on classes +<rsi>,<mic>, +<disk>,<ab>and +<mo>Added argument
excessto thekurtosis()+function (defaults toFALSE), to return the excess +kurtosis, defined as the kurtosis minus three.Other
-- Removed functions
portion_R(),portion_S()andportion_I()that were deprecated since version 0.9.0 (November 2019) and were replaced withproportion_R(),proportion_S()andproportion_I()+- Removed functions
portion_R(),portion_S()+andportion_I()that were deprecated since version 0.9.0 +(November 2019) and were replaced withproportion_R(), +proportion_S()andproportion_I() - Removed unnecessary references to the
basepackage
- - Added packages that could be useful for some functions to the
Suggestsfield of theDESCRIPTIONfile
+ - Added packages that could be useful for some functions to the
+
Suggestsfield of theDESCRIPTIONfile
- Removed functions
Function
ab_from_text()to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it usesas.ab()internally
+Function
ab_from_text()to retrieve antimicrobial +drug names, doses and forms of administration from clinical texts in +e.g. health care records, which also corrects for misspelling since it +usesas.ab()internally-
-
Tidyverse selection helpers for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like
+dplyr::select()andtidyr::pivot_longer():Tidyverse +selection helpers for antibiotic classes, that help to select the +columns of antibiotics that are of a specific antibiotic class, without +the need to define the columns or antibiotic abbreviations. They can be +used in any function that allows selection helpers, like +
dplyr::select()andtidyr::pivot_longer():library(dplyr) @@ -698,54 +1144,105 @@ select(carbapenems()) #> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
- Added
mo_domain()as an alias tomo_kingdom()
-Added function
filter_penicillins()to filter isolates on a specific result in any column with a name in the antimicrobial ‘penicillins’ class (more specific: ATC subgroup Beta-lactam antibacterials, penicillins)
-Added official antimicrobial names to all
filter_ab_class()functions, such asfilter_aminoglycosides()
-Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the
antibioticsdata set
+Added
mo_domain()as an alias to +mo_kingdom()
+Added function
filter_penicillins()to filter +isolates on a specific result in any column with a name in the +antimicrobial ‘penicillins’ class (more specific: ATC subgroup +Beta-lactam antibacterials, penicillins)
+Added official antimicrobial names to all +
filter_ab_class()functions, such as +filter_aminoglycosides()
+Added antibiotics code “FOX1” for cefoxitin screening +(abbreviation “cfsc”) to the
antibioticsdata setAdded Monuril as trade name for fosfomycin
-Added argument
conserve_capped_valuestoas.rsi()for interpreting MIC values - it makes sure that values starting with “<” (but not “<=”) will always return “S” and values starting with “>” (but not “>=”) will always return “R”. The default behaviour ofas.rsi()has not changed, so you need to specifically doas.rsi(..., conserve_capped_values = TRUE).
+Added argument
conserve_capped_valuesto +as.rsi()for interpreting MIC values - it makes sure that +values starting with “<” (but not “<=”) will always return “S” and +values starting with “>” (but not “>=”) will always return “R”. +The default behaviour ofas.rsi()has not changed, so you +need to specifically do +as.rsi(..., conserve_capped_values = TRUE).-
-
Big speed improvement for using any function on microorganism codes from earlier package versions (prior to
-AMRv1.2.0), such asas.mo(),mo_name(),first_isolate(),eucast_rules(),mdro(), etc.As a consequence, very old microbial codes (from
+AMRv0.5.0 and lower) are not supported anymore. Useas.mo()on your microorganism names or codes to transform them to current abbreviations used in this package.Big speed improvement for using any function on microorganism +codes from earlier package versions (prior to
+AMRv1.2.0), +such asas.mo(),mo_name(), +first_isolate(),eucast_rules(), +mdro(), etc.As a consequence, very old microbial codes (from
AMR+v0.5.0 and lower) are not supported anymore. Use +as.mo()on your microorganism names or codes to transform +them to current abbreviations used in this package. -
-
Improvements for
-susceptibility()andresistance()and allcount_*(),proportion_*()functions:- 95% speed improvement by using other base R functions for calculation -
- Using unexisting columns wil now return an error instead of dropping them silently -
- Using variables for column names (as well as selectors like
dplyr::all_of()) now works again
+ - 95% speed improvement by using other base R functions for +calculation +
- Using unexisting columns wil now return an error instead of dropping +them silently +
- Using variables for column names (as well as selectors like
+
dplyr::all_of()) now works again
Improvements for
+susceptibility()and +resistance()and allcount_*(), +proportion_*()functions: -
Improvements for
-as.ab():- Dramatic improvement of the algorithm behind
as.ab(), making many more input errors translatable, such as digitalised health care records, using too few or too many vowels or consonants and many more
+ - Dramatic improvement of the algorithm behind
as.ab(), +making many more input errors translatable, such as digitalised health +care records, using too few or too many vowels or consonants and many +more - Added progress bar -
- Fixed a bug where
as.ab()would return an error on invalid input values
- - The
as.ab()function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
+ - Fixed a bug where
as.ab()would return an error on +invalid input values
+ - The
as.ab()function will now throw a note if more than +1 antimicrobial drug could be retrieved from a single input value.
- - Dramatic improvement of the algorithm behind
Fixed a bug where
eucast_rules()would not work on a tibble when thetibbleordplyrpackage was loaded
-Fixed a bug for CLSI 2019 guidelines (using
as.rsi()), that also included results for animals. It now only contains interpretation guidelines for humans.
-All
*_join_microorganisms()functions andbug_drug_combinations()now return the original data class (e.g.tibbles anddata.tables)
+Fixed a bug where
eucast_rules()would not work on a +tibble when thetibbleordplyrpackage was +loaded
+Fixed a bug for CLSI 2019 guidelines (using +
as.rsi()), that also included results for animals. It now +only contains interpretation guidelines for humans.
+All
*_join_microorganisms()functions and +bug_drug_combinations()now return the original data class +(e.g.tibbles anddata.tables)-
-
For functions
+rsi_df(),proportion_df()andcount_df():For functions
rsi_df(),proportion_df()+andcount_df():- Fixed a bug for using grouped versions -
- Fixed a bug where not all different antimicrobial results were added as rows -
- Fixed a bug when only calculating counts (
count_df()) when all antibiotics in the data set have onlyNAs
+ - Fixed a bug where not all different antimicrobial results were added +as rows +
- Fixed a bug when only calculating counts (
count_df()) +when all antibiotics in the data set have onlyNAs
- Improved auto-determination for columns of types
<mo>and<Date>
-Fixed a bug in
bug_drug_combinations()for when only one antibiotic was in the input data
-Changed the summary for class
<rsi>, to highlight the %SI vs. %R
-Improved error handling, giving more useful info when functions return an error
-Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
-Speed improvement for
mdro()andfilter_ab_class()
-New option
arrows_textangledforggplot_pca()to indicate whether the text at the end of the arrows should be angled (defaults toTRUE, as it was in previous versions)
+Improved auto-determination for columns of types +
<mo>and<Date>
+Fixed a bug in
bug_drug_combinations()for when only +one antibiotic was in the input data
+Changed the summary for class
<rsi>, to +highlight the %SI vs. %R
+Improved error handling, giving more useful info when functions +return an error
+Any progress bar will now only show in interactive mode (i.e. not +in R Markdown)
+Speed improvement for
mdro()and +filter_ab_class()
+New option
arrows_textangledfor +ggplot_pca()to indicate whether the text at the end of the +arrows should be angled (defaults toTRUE, as it was in +previous versions)Added parenteral DDD to benzylpenicillin
-Fixed a bug where
as.mic()could not handle dots without a leading zero (like"<=.25)
+Fixed a bug where
as.mic()could not handle dots +without a leading zero (like"<=.25)- Moved primary location of this project from GitLab to GitHub, giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI. +
- Moved primary location of this project from GitLab to GitHub, giving us native +support for automated syntax checking without being dependent on +external services such as AppVeyor and Travis CI.
-
-
Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
-Making this package independent of especially the tidyverse (e.g. packages
+dplyrandtidyr) 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.Removed code dependency on all other R packages, making this +package fully independent of the development process of others. This is +a major code change, but will probably not be noticeable by most +users.
+Making this package independent of especially the tidyverse +(e.g. packages
dplyrandtidyr) 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:
-- Function
freq()that was borrowed from thecleanerpackage was removed. Usecleaner::freq(), or runlibrary("cleaner")before you usefreq().
- Printing values of classmoorrsiin a tibble will no longer be in colour and printingrsiin a tibble will show the class<ord>, not<rsi>anymore. This is purely a visual effect.
-All functions from themo_*family (likemo_name()andmo_gramstain()) are noticeably slower when running on hundreds of thousands of rows.
-- For developers: classes
moandabnow both also inherit classcharacter, to support any data transformation. This change invalidates code that checks for class length == 1.
+ - Function
freq()that was borrowed from the +cleanerpackage was removed. Use +cleaner::freq(), or runlibrary("cleaner")+before you usefreq().
+ Printing values of classmoorrsiin +a tibble will no longer be in colour and printingrsiin a +tibble will show the class<ord>, not +<rsi>anymore. This is purely a visual +effect.
+All functions from themo_*family (like +mo_name()andmo_gramstain()) are noticeably +slower when running on hundreds of thousands of rows.
+- For developers: classes
moandabnow both +also inherit classcharacter, to support any data +transformation. This change invalidates code that checks for class +length == 1.
- Function
- Taxonomy:
-
- Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using
first_isolate()), since some bacterial names might be renamed to other genera or other (sub)species. This is expected behaviour.
- - Removed the Catalogue of Life IDs (like 776351), since they now work with a species ID (hexadecimal string) +
- Updated the taxonomy of microorganisms to May 2020, using the
+Catalogue of Life (CoL), the Global Biodiversity Information Facility
+(GBIF) and the List of Prokaryotic names with Standing in Nomenclature
+(LPSN, hosted by DSMZ since February 2020). Note: a
+taxonomic update may always impact determination of first isolates
+(using
first_isolate()), since some bacterial names might +be renamed to other genera or other (sub)species. This is expected +behaviour.
+ - Removed the Catalogue of Life IDs (like 776351), since they now work +with a species ID (hexadecimal string)
- Updated the taxonomy of microorganisms to May 2020, using the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF) and the List of Prokaryotic names with Standing in Nomenclature (LPSN, hosted by DSMZ since February 2020). Note: a taxonomic update may always impact determination of first isolates (using
- EUCAST rules:
-
- The
eucast_rules()function no longer applies “other” rules at default that are made available by this package (like setting ampicillin = R when ampicillin + enzyme inhibitor = R). The default input value forrulesis nowc("breakpoints", "expert")instead of"all", but this can be changed by the user. To return to the old behaviour, setoptions(AMR.eucast_rules = "all").
- - Fixed a bug where checking antimicrobial results in the original data were not regarded as valid R/SI values -
- All “other” rules now apply for all drug combinations in the
antibioticsdata set these two rules: -- A drug with enzyme inhibitor will be set to S if the drug without enzyme inhibitor is S -
- A drug without enzyme inhibitor will be set to R if the drug with enzyme inhibitor is R +
- The
eucast_rules()function no longer applies “other” +rules at default that are made available by this package (like setting +ampicillin = R when ampicillin + enzyme inhibitor = R). The default +input value forrulesis now +c("breakpoints", "expert")instead of"all", +but this can be changed by the user. To return to the old behaviour, set +options(AMR.eucast_rules = "all").
+ - Fixed a bug where checking antimicrobial results in the original +data were not regarded as valid R/SI values +
- All “other” rules now apply for all drug combinations in the
+
antibioticsdata set these two rules: +- A drug with enzyme inhibitor will be set to S if +the drug without enzyme inhibitor is S +
- A drug without enzyme inhibitor will be set to R if +the drug with enzyme inhibitor is R
- - Added official drug names to verbose output of
eucast_rules()+This works for all drug combinations, such as ampicillin/sulbactam, +ceftazidime/avibactam, trimethoprim/sulfamethoxazole, etc.
+ - Added official drug names to verbose output of
+
eucast_rules()
- - Added function
ab_url()to return the direct URL of an antimicrobial agent from the official WHO website
- - Improvements for algorithm in
as.ab(), so that e.g.as.ab("ampi sul")andab_name("ampi sul")work
- - Functions
ab_atc()andab_group()now returnNAif no antimicrobial agent could be found
- - Small fix for some text input that could not be coerced as valid MIC values -
- Fix for interpretation of generic CLSI interpretation rules (thanks to Anthony Underwood) -
- Fix for
set_mo_source()to make sure that columnmowill always be the second column
- - Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam +
- Added function
ab_url()to return the direct URL of an +antimicrobial agent from the official WHO website
+ - Improvements for algorithm in
as.ab(), so that +e.g.as.ab("ampi sul")andab_name("ampi sul")+work
+ - Functions
ab_atc()andab_group()now +returnNAif no antimicrobial agent could be found
+ - Small fix for some text input that could not be coerced as valid MIC +values +
- Fix for interpretation of generic CLSI interpretation rules (thanks +to Anthony Underwood) +
- Fix for
set_mo_source()to make sure that column +mowill always be the second column
+ - Added abbreviation “cfsc” for Cefoxitin and “cfav” for +Ceftazidime/avibactam
- The
- Removed previously deprecated function
p.symbol()- it was replaced withp_symbol()+- Removed previously deprecated function
p.symbol()- it +was replaced withp_symbol()
- - Removed function
read.4d(), that was only useful for reading data from an old test database.
+ - Removed function
read.4d(), that was only useful for +reading data from an old test database.
- Removed previously deprecated function
- Support for easy principal component analysis for AMR, using the new
pca()function
- - Plotting biplots for principal component analysis using the new
ggplot_pca()function
+ - Support for easy principal component analysis for AMR, using the new
+
pca()function
+ - Plotting biplots for principal component analysis using the new
+
ggplot_pca()function - Improvements for the algorithm used by
as.mo()(and consequently allmo_*functions, that useas.mo()internally): -- Support for codes ending with
SPEfor species, like"ESCSPE"for Escherichia coli +- Improvements for the algorithm used by
as.mo()(and +consequently allmo_*functions, that use +as.mo()internally): +- Support for codes ending with
SPEfor species, like +"ESCSPE"for Escherichia coli
- - Support for any encoding, which means that any language-specific character with accents can be used for input -
- Support for more arbitrary IDs used in laboratory information systems +
- Support for any encoding, which means that any language-specific +character with accents can be used for input +
- Support for more arbitrary IDs used in laboratory information +systems
- Small fix for preventing viruses being treated as bacteria -
- Small fix for preventing contamination and lack of growth being treated as valid microorganisms +
- Small fix for preventing contamination and lack of growth being +treated as valid microorganisms
- - Support for codes ending with
- Support for all abbreviations of antibiotics and antimycotics used by the Netherlands National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM) -
- Added more abbreviations to the
antibioticsdata set
- - Reloaded original EUCAST master tables from 2019 (2020 was already available). This seems more reliable than the data we used from WHONET. -
- Added generic CLSI rules for R/SI interpretation using
as.rsi()for years 2010-2019 (thanks to Anthony Underwood)
+ - Support for all abbreviations of antibiotics and antimycotics used +by the Netherlands National Institute for Public Health and the +Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM) +
- Added more abbreviations to the
antibioticsdata +set
+ - Reloaded original EUCAST master tables from 2019 (2020 was already +available). This seems more reliable than the data we used from +WHONET. +
- Added generic CLSI rules for R/SI interpretation using
+
as.rsi()for years 2010-2019 (thanks to Anthony +Underwood)
- Improvements for the algorithm used by
- Support for codes ending with
Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
+Fixed important floating point error for some MIC comparisons in +EUCAST 2020 guideline
-
-
Interpretation from MIC values (and disk zones) to R/SI can now be used with
+mutate_at()of thedplyrpackage:Interpretation from MIC values (and disk zones) to R/SI can now +be used with
mutate_at()of thedplyr+package:
- Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole
-Added
uti(as abbreviation of urinary tract infections) as argument toas.rsi(), so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
-Info printing in functions
eucast_rules(),first_isolate(),mdro()andresistance_predict()will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
+Added antibiotic abbreviations for a laboratory manufacturer +(GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and +trimethoprim/sulfamethoxazole
+Added
uti(as abbreviation of urinary tract +infections) as argument toas.rsi(), so interpretation of +MIC values and disk zones can be made dependent on isolates specifically +from UTIs
+Info printing in functions
eucast_rules(), +first_isolate(),mdro()and +resistance_predict()will now at default only print when R +is in an interactive mode (i.e. not in RMarkdown)
AMR 1.4.02020-10-08
New
-Changed
-AMR 1.3.02020-07-31
New
-Changed
Other
-Breaking
Changed
Other
-AMR 1.1.02020-04-15
New
-Changed
-AMR 1.0.12020-02-23
Changed
-AMR 1.0.02020-02-17
-This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
+This software is now out of beta and considered stable. Nonetheless, +this package will be developed continually.
New
-- Support for the newest EUCAST Clinical Breakpoint Tables v.10.0, valid from 1 January 2020. This affects translation of MIC and disk zones using
as.rsi()and inferred resistance and susceptibility usingeucast_rules().
- - The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt. This allows for machine reading these guidelines, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file can be found here. +
- Support for the newest EUCAST Clinical
+Breakpoint Tables v.10.0, valid from 1 January 2020. This affects
+translation of MIC and disk zones using
as.rsi()and +inferred resistance and susceptibility using +eucast_rules().
+ - The repository of this package now contains a clean version of the +EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk +diffusion values to R/SI: https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt. +This allows for machine reading these guidelines, which +is almost impossible with the Excel and PDF files distributed by EUCAST +and CLSI. This file used to process the EUCAST Clinical Breakpoints +Excel file can +be found here.
- Support for LOINC and SNOMED codes
-
-
Support for LOINC codes in the
+antibioticsdata set. Useab_loinc()to retrieve LOINC codes, or use a LOINC code for input in anyab_*function:Support for LOINC codes in the
antibioticsdata set. +Useab_loinc()to retrieve LOINC codes, or use a LOINC code +for input in anyab_*function:ab_loinc("ampicillin") @@ -863,7 +1456,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ #> [1] "J01CA01" -
-
Support for SNOMED CT codes in the
+microorganismsdata set. Usemo_snomed()to retrieve SNOMED codes, or use a SNOMED code for input in anymo_*function:Support for SNOMED CT codes in the
microorganisms+data set. Usemo_snomed()to retrieve SNOMED codes, or use +a SNOMED code for input in anymo_*function:mo_snomed("S. aureus") @@ -877,25 +1472,47 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Changes
-- The
as.mo()function previously wrote to the package folder to improve calculation speed for previously calculated results. This is no longer the case, to comply with CRAN policies. Consequently, the functionclear_mo_history()was removed.
- - Bugfix for some WHONET microorganism codes that were not interpreted correctly when using
as.rsi()+- The
as.mo()function previously wrote to the package +folder to improve calculation speed for previously calculated results. +This is no longer the case, to comply with CRAN policies. Consequently, +the functionclear_mo_history()was removed.
+ - Bugfix for some WHONET microorganism codes that were not interpreted
+correctly when using
as.rsi()
- - Improvements for the algorithm used by
as.mo()(and consequently allmo_*functions, that useas.mo()internally): -- Support for missing spaces, e.g. in
as.mo("Methicillin-resistant S.aureus")+ - Improvements for the algorithm used by
as.mo()(and +consequently allmo_*functions, that use +as.mo()internally): +- Support for missing spaces, e.g. in
+
as.mo("Methicillin-resistant S.aureus") - Better support for determination of Salmonella biovars -
- Speed improvements, especially for the G. species format (G for genus), like E. coli and K pneumoniae +
- Speed improvements, especially for the G. species format (G +for genus), like E. coli and K pneumoniae -
- Support for more common codes used in laboratory information systems +
- Support for more common codes used in laboratory information +systems
- - Support for missing spaces, e.g. in
+
- Input values for
as.disk()limited to a maximum of 50 millimeters
- - Added a lifecycle state to every function, following the lifecycle circle of the
tidyverse+ - Input values for
as.disk()limited to a maximum of 50 +millimeters
+ - Added a lifecycle state to every function, following the lifecycle
+circle of the
tidyverse
- - For in
as.ab(): support for drugs starting with “co-” like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks to Peter Dutey)
- - Changes to the
antibioticsdata set (thanks to Peter Dutey): -- Added more synonyms to colistin, imipenem and piperacillin/tazobactam -
- Moved synonyms Rifinah and Rimactazid from rifampicin (
RIF) to rifampicin/isoniazid (RFI). Please note that the combination rifampicin/isoniazid has no DDDs defined, so e.g.ab_ddd("Rimactazid")will now returnNA.
- - Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole (
SMX) to trimethoprim/sulfamethoxazole (SXT)
+ - For in
as.ab(): support for drugs starting with “co-” +like co-amoxiclav, co-trimoxazole, co-trimazine and co-trimazole (thanks +to Peter Dutey)
+ - Changes to the
antibioticsdata set (thanks to Peter +Dutey): +- Added more synonyms to colistin, imipenem and +piperacillin/tazobactam +
- Moved synonyms Rifinah and Rimactazid from rifampicin
+(
RIF) to rifampicin/isoniazid (RFI). Please +note that the +combination rifampicin/isoniazid has no DDDs defined, so +e.g.ab_ddd("Rimactazid")will now return +NA.
+ - Moved synonyms Bactrimel and Cotrimazole from sulfamethoxazole
+(
SMX) to trimethoprim/sulfamethoxazole +(SXT)
- Support for missing spaces, e.g. in
- The
@@ -909,9 +1526,19 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/AMR 0.9.02019-11-29
@@ -996,14 +1663,24 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Breaking
-- Adopted Adeolu et al. (2016), PMID 27620848 for the
microorganismsdata set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like Morganellaceae and Yersiniaceae). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations withmdro()will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family. +- Adopted Adeolu et al. (2016), PMID 27620848 for
+the
microorganismsdata set, which means that the new order +Enterobacterales now consists of a part of the existing family +Enterobacteriaceae, but that this family has been split into other +families as well (like Morganellaceae and +Yersiniaceae). Although published in 2016, this information is +not yet in the Catalogue of Life version of 2019. All MDRO +determinations withmdro()will now use the +Enterobacterales order for all guidelines before 2016 that were +dependent on the Enterobacteriaceae family.-
-
If you were dependent on the old Enterobacteriaceae family e.g. by using in your code:
+If you were dependent on the old Enterobacteriaceae family +e.g. by using in your code:
@@ -925,7 +1552,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/if (mo_family(somebugs) == "Enterobacteriaceae") ...New
-
-
Functions
+susceptibility()andresistance()as aliases ofproportion_SI()andproportion_R(), respectively. These functions were added to make it more clear that “I” should be considered susceptible and not resistant.Functions
susceptibility()and +resistance()as aliases ofproportion_SI()and +proportion_R(), respectively. These functions were added to +make it more clear that “I” should be considered susceptible and not +resistant. -
-
Support for a new MDRO guideline: Magiorakos AP, Srinivasan A et al. “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).
-- This is now the new default guideline for the
mdro()function
- - The new Verbose mode (
mdro(...., verbose = TRUE)) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents
+ - This is now the new default guideline for the
mdro()+function
+ - The new Verbose mode (
mdro(...., verbose = TRUE)) +returns an informative data set where the reason for MDRO determination +is given for every isolate, and an list of the resistant antimicrobial +agents
Support for a new MDRO guideline: Magiorakos AP, Srinivasan A +et al. “Multidrug-resistant, extensively drug-resistant and +pandrug-resistant bacteria: an international expert proposal for interim +standard definitions for acquired resistance.” Clinical Microbiology and +Infection (2012).
+
- - This is now the new default guideline for the
Data set
antivirals, containing all entries from the ATC J05 group with their DDDs for oral and parenteral treatment
+Data set
antivirals, containing all entries from the +ATC J05 group with their DDDs for oral and parenteral treatment
Changes
- Improvements to algorithm in
as.mo(): -Now allows “ou” where “au” should have been used and vice versa
-More intelligent way of coping with some consonants like “l” and “r”
+Now allows “ou” where “au” should have been used and vice +versa
+More intelligent way of coping with some consonants like “l” and +“r”
-
-
Added a score (a certainty percentage) to
+mo_uncertainties(), that is calculated using the Levenshtein distance:Added a score (a certainty percentage) to +
mo_uncertainties(), that is calculated using the Levenshtein +distance:
- - Removed previously deprecated function
as.atc()- this function was replaced byab_atc()+ - Removed previously deprecated function
as.atc()- this +function was replaced byab_atc()
- - Renamed all
portion_*functions toproportion_*. Allportion_*functions are still available as deprecated functions, and will return a warning when used.
- - When running
as.rsi()over a data set, it will now print the guideline that will be used if it is not specified by the user
+ - Renamed all
portion_*functions to +proportion_*. Allportion_*functions are +still available as deprecated functions, and will return a warning when +used.
+ - When running
as.rsi()over a data set, it will now +print the guideline that will be used if it is not specified by the +user - Improvements for
eucast_rules(): -- Fix where Stenotrophomonas maltophilia would always become ceftazidime R (following EUCAST v3.1) -
- Fix where Leuconostoc and Pediococcus would not always become glycopeptides R -
- non-EUCAST rules in
eucast_rules()are now applied first and not as last anymore. This is to improve the dependency on certain antibiotics for the official EUCAST rules. Please see?eucast_rules.
+ - Fix where Stenotrophomonas maltophilia would always become +ceftazidime R (following EUCAST v3.1) +
- Fix where Leuconostoc and Pediococcus would not +always become glycopeptides R +
- non-EUCAST rules in
eucast_rules()are now applied +first and not as last anymore. This is to improve the dependency on +certain antibiotics for the official EUCAST rules. Please see +?eucast_rules.
- - Fix for interpreting MIC values with
as.rsi()where the input isNA+ - Fix for interpreting MIC values with
as.rsi()where the +input isNA
- - Added “imi” and “imp” as allowed abbreviation for Imipenem (IPM) -
- Fix for automatically determining columns with antibiotic results in
mdro()andeucast_rules()+ - Added “imi” and “imp” as allowed abbreviation for Imipenem +(IPM) +
- Fix for automatically determining columns with antibiotic results in
+
mdro()andeucast_rules()
- - Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the
antibioticsdata set
+ - Added ATC codes for ceftaroline, ceftobiprole and faropenem and
+fixed two typos in the
antibioticsdata set - More robust way of determining valid MIC values -
- Small changed to the
example_isolatesdata set to better reflect reality
- - Added more microorganisms codes from laboratory systems (esp. species of Pseudescherichia and Rodentibacter) +
- Small changed to the
example_isolatesdata set to +better reflect reality
+ - Added more microorganisms codes from laboratory systems +(esp. species of Pseudescherichia and +Rodentibacter)
- Added Gram-stain to
mo_info()
Other
-- Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great Roxygen2, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed. -
- Change dependency on
cleantocleaner, as this package was renamed accordingly upon CRAN request
+ - Rewrote the complete documentation to markdown format, to be able to +use the very latest version of the great Roxygen2, released in +November 2019. This tremously improved the documentation quality, since +the rewrite forced us to go over all texts again and make changes where +needed. +
- Change dependency on
cleantocleaner, as +this package was renamed accordingly upon CRAN request - Added Dr. Sofia Ny as contributor
-
-
-
-
- Adopted Adeolu et al. (2016), PMID 27620848 for
+the
Breaking
-
-
Determination of first isolates now excludes all ‘unknown’ microorganisms at default, i.e. microbial code
+"UNKNOWN". They can be included with the new argumentinclude_unknown:Determination of first isolates now excludes all +‘unknown’ microorganisms at default, i.e. microbial code +
"UNKNOWN". They can be included with the new argument +include_unknown:-first_isolate(..., include_unknown = TRUE)For WHONET users, this means that all records/isolates with organism code
+"con"(contamination) will be excluded at default, sinceas.mo("con") = "UNKNOWN". The function always shows a note with the number of ‘unknown’ microorganisms that were included or excluded.For WHONET users, this means that all records/isolates with organism +code
"con"(contamination) will be excluded at +default, sinceas.mo("con") = "UNKNOWN". The function +always shows a note with the number of ‘unknown’ microorganisms that +were included or excluded. -
-
For code consistency, classes
+abandmowill now be preserved in any subsetting or assignment. For the sake of data integrity, this means that invalid assignments will now result inNA:For code consistency, classes
abandmo+will now be preserved in any subsetting or assignment. For the sake of +data integrity, this means that invalid assignments will now result in +NA:-# how it works in base R: @@ -1017,15 +1694,26 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ x[1] <- "testvalue" #> Warning message: #> invalid microorganism code, NA generatedThis 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.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. Thefreq()function still works, since it is re-exported from thecleanpackage (which will be installed automatically upon updating thisAMRpackage).
-Renamed data set
septic_patientstoexample_isolates
+Function
freq()has moved to a new package,clean(CRAN link), since +creating frequency tables actually does not fit the scope of this +package. Thefreq()function still works, since it is +re-exported from thecleanpackage (which will be installed +automatically upon updating thisAMRpackage).
+Renamed data set
septic_patientsto +example_isolates
@@ -1144,7 +1904,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/New
-
-
Function
+bug_drug_combinations()to quickly get adata.framewith the results of all bug-drug combinations in a data set. The column containing microorganism codes is guessed automatically and its input is transformed withmo_shortname()at default:Function
bug_drug_combinations()to quickly get a +data.framewith the results of all bug-drug combinations in +a data set. The column containing microorganism codes is guessed +automatically and its input is transformed with +mo_shortname()at default:-x <- bug_drug_combinations(example_isolates) @@ -1048,13 +1736,25 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ #> 3 Gram-negative AMP 227 0 405 632 #> 4 Gram-negative AMX 227 0 405 632 #> NOTE: Use 'format()' on this result to get a publicable/printable format.You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R
+format()function:You can format this to a printable format, ready for reporting or +exporting to e.g. Excel with the base R
format()+function:format(x, combine_IR = FALSE) -
-
Additional way to calculate co-resistance, i.e. when using multiple antimicrobials as input for
+portion_*functions orcount_*functions. This can be used to determine the empiric susceptibility of a combination therapy. A new argumentonly_all_tested(which defaults toFALSE) replaces the oldalso_single_testedand 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 theportionandcounthelp pages), where the %SI is being determined:Additional way to calculate co-resistance, i.e. when using +multiple antimicrobials as input for
portion_*functions or +count_*functions. This can be used to determine the +empiric susceptibility of a combination therapy. A new argument +only_all_tested(which defaults to +FALSE) replaces the old +also_single_testedand 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 theportion+andcounthelp pages), where the %SI is being +determined:-# -------------------------------------------------------------------- @@ -1073,10 +1773,18 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # R <NA> - - - - # <NA> <NA> - - - - # --------------------------------------------------------------------Since this is a major change, usage of the old
+also_single_testedwill throw an informative error that it has been replaced byonly_all_tested.Since this is a major change, usage of the old +
also_single_testedwill throw an informative error that it +has been replaced byonly_all_tested. -
-
+tibbleprinting support for classesrsi,mic,disk,abmo. When usingtibbles containing antimicrobial columns, valuesSwill print in green, valuesIwill print in yellow and valuesRwill print in red. Microbial IDs (classmo) will emphasise on the genus and species, not on the kingdom.tibbleprinting support for classes +rsi,mic,disk,ab+mo. When usingtibbles containing +antimicrobial columns, valuesSwill print in green, values +Iwill print in yellow and valuesRwill print +in red. Microbial IDs (classmo) will emphasise on the +genus and species, not on the kingdom.# (run this on your own console, as this page does not support colour printing) @@ -1088,44 +1796,93 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/Changed
-- Many algorithm improvements for
as.mo()(of which some led to additions to themicroorganismsdata set). Many thanks to all contributors that helped improving the algorithms. -- Self-learning algorithm - the function now gains experience from previously determined microorganism IDs and learns from it (yielding 80-95% speed improvement for any guess after the first try) +
- Many algorithm improvements for
as.mo()(of which some +led to additions to themicroorganismsdata set). Many +thanks to all contributors that helped improving the algorithms. +- Self-learning algorithm - the function now gains experience from +previously determined microorganism IDs and learns from it (yielding +80-95% speed improvement for any guess after the first try)
- Big improvement for misspelled input -
- These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus -
- Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology -
- Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS) +
- These new trivial names known to the field are now understood: +meningococcus, gonococcus, pneumococcus +
- Updated to the latest taxonomic data (updated to August 2019, from +the International Journal of Systematic and Evolutionary +Microbiology +
- Added support for Viridans Group Streptococci (VGS) and Milleri +Group Streptococci (MGS)
- Added support for Blastocystis
- Added support for 5,000 new fungi
- Added support for unknown yeasts and fungi -
- Changed most microorganism IDs to improve readability. For example, the old code
B_ENTRC_FAEcould have been both E. faecalis and E. faecium. Its new code isB_ENTRC_FCLSand E. faecium has becomeB_ENTRC_FACM. Also, the Latin character ae is now preserved at the start of each genus and species abbreviation. For example, the old code for Aerococcus urinae wasB_ARCCC_NAE. This is nowB_AERCC_URIN. IMPORTANT: Old microorganism IDs are still supported, but support will be dropped in a future version. Useas.mo()on your old codes to transform them to the new format. Using functions from themo_*family (likemo_name()andmo_gramstain()) on old codes, will throw a warning.
+ - Changed most microorganism IDs to improve readability. For example,
+the old code
B_ENTRC_FAEcould have been both E. +faecalis and E. faecium. Its new code is +B_ENTRC_FCLSand E. faecium has become +B_ENTRC_FACM. Also, the Latin character ae is now preserved +at the start of each genus and species abbreviation. For example, the +old code for Aerococcus urinae wasB_ARCCC_NAE. +This is nowB_AERCC_URIN. IMPORTANT: Old +microorganism IDs are still supported, but support will be dropped in a +future version. Useas.mo()on your old codes to transform +them to the new format. Using functions from themo_*+family (likemo_name()andmo_gramstain()) on +old codes, will throw a warning.
- - More intelligent guessing for
as.ab(), including bidirectional language support
- - Added support for the German national guideline (3MRGN/4MRGN) in the
mdro()function, to determine multi-drug resistant organisms
+ - More intelligent guessing for
as.ab(), including +bidirectional language support
+ - Added support for the German national guideline (3MRGN/4MRGN) in the
+
mdro()function, to determine multi-drug resistant +organisms - Function
eucast_rules():- Fixed a bug for Yersinia pseudotuberculosis
- Added more informative errors and warnings
- Printed info now distinguishes between added and changes values -
- Using Verbose mode (i.e.
eucast_rules(..., verbose = TRUE)) returns more informative and readable output
- - Using factors as input now adds missing factors levels when the function changes antibiotic results +
- Using Verbose mode
+(i.e.
eucast_rules(..., verbose = TRUE)) returns more +informative and readable output
+ - Using factors as input now adds missing factors levels when the +function changes antibiotic results
- - Improved the internal auto-guessing function for determining antimicrobials in your data set (
AMR:::get_column_abx())
- - Removed class
atc- usingas.atc()is now deprecated in favour ofab_atc()and this will return a character, not theatcclass anymore
- - Removed deprecated functions
abname(),ab_official(),atc_name(),atc_official(),atc_property(),atc_tradenames(),atc_trivial_nl()+ - Improved the internal auto-guessing function for determining
+antimicrobials in your data set
+(
AMR:::get_column_abx())
+ - Removed class
atc- usingas.atc()is now +deprecated in favour ofab_atc()and this will return a +character, not theatcclass anymore
+ - Removed deprecated functions
abname(), +ab_official(),atc_name(), +atc_official(),atc_property(), +atc_tradenames(),atc_trivial_nl() - Fix and speed improvement for
mo_shortname()
- - Fix for using
mo_*functions where the coercion uncertainties and failures would not be available throughmo_uncertainties()andmo_failures()anymore
- - Deprecated the
countryargument ofmdro()in favour of the already existingguidelineargument to support multiple guidelines within one country
- - The
nameofRIFis now Rifampicin instead of Rifampin
- - The
antibioticsdata set is now sorted by name and all cephalosporins now have their generation between brackets
- - Speed improvement for
guess_ab_col()which is now 30 times faster for antibiotic abbreviations
- - Improved
filter_ab_class()to be more reliable and to support 5th generation cephalosporins
- - Function
availability()now usesportion_R()instead ofportion_IR(), to comply with EUCAST insights
- - Functions
age()andage_groups()now have ana.rmargument to remove empty values
- - Renamed function
p.symbol()top_symbol()(the former is now deprecated and will be removed in a future version)
- - Using negative values for
xinage_groups()will now introduceNAs and not return an error anymore
+ - Fix for using
mo_*functions where the coercion +uncertainties and failures would not be available through +mo_uncertainties()andmo_failures()+anymore
+ - Deprecated the
countryargument ofmdro()+in favour of the already existingguidelineargument to +support multiple guidelines within one country
+ - The
nameofRIFis now Rifampicin instead +of Rifampin
+ - The
antibioticsdata set is now sorted by name and all +cephalosporins now have their generation between brackets
+ - Speed improvement for
guess_ab_col()which is now 30 +times faster for antibiotic abbreviations
+ - Improved
filter_ab_class()to be more reliable and to +support 5th generation cephalosporins
+ - Function
availability()now uses +portion_R()instead ofportion_IR(), to comply +with EUCAST insights
+ - Functions
age()andage_groups()now have +ana.rmargument to remove empty values
+ - Renamed function
p.symbol()top_symbol()+(the former is now deprecated and will be removed in a future +version)
+ - Using negative values for
xin +age_groups()will now introduceNAs and not +return an error anymore - Fix for determining the system’s language
- Fix for
key_antibiotics()on foreign systems - Added 80 new LIS codes for microorganisms @@ -1134,8 +1891,11 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
- Added more MIC factor levels (
as.mic()) - Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors -
- Cleaned the coding style of every single syntax line in this package with the help of the
lintrpackage
+ - Added Prof. Dr. Casper Albers as doctoral advisor and added +Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis +Souverein and Annick Lenglet as contributors +
- Cleaned the coding style of every single syntax line in this package
+with the help of the
lintrpackage
Other
-
- Many algorithm improvements for
-New
-
-
Function
+rsi_df()to transform adata.frameto 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 functionscount_df()andportion_df()to immediately show resistance percentages and number of available isolates:Function
rsi_df()to transform a +data.frameto 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 functionscount_df()and +portion_df()to immediately show resistance percentages and +number of available isolates:septic_patients %>% @@ -1157,7 +1923,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # 4 Ciprofloxacin R 0.1618169 228 -
-
Support for all scientifically published pathotypes of E. coli to date (that we could find). Supported are:
+Support for all scientifically published pathotypes of E. +coli to date (that we could find). Supported are:
- AIEC (Adherent-Invasive E. coli)
- ATEC (Atypical Entero-pathogenic E. coli)
- DAEC (Diffusely Adhering E. coli) @@ -1179,31 +1946,52 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ mo_gramstain("EHEC") # "Gram-negative"
Function
mo_info()as an analogy toab_info(). Themo_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 microorganismFunction
mo_info()as an analogy to +ab_info(). Themo_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 microorganismChanged
-- Column names of output
count_df()andportion_df()are now lowercase
+ - Column names of output
count_df()and +portion_df()are now lowercase - Fixed bug in translation of microorganism names
- Fixed bug in determining taxonomic kingdoms -
- Algorithm improvements for
as.ab()andas.mo()to understand even more severely misspelled input
- - Function
as.ab()now allows spaces for coercing antibiotics names
- - Added
ggplot2methods for automatically determining the scale type of classesmoandab+ - Algorithm improvements for
as.ab()and +as.mo()to understand even more severely misspelled +input
+ - Function
as.ab()now allows spaces for coercing +antibiotics names
+ - Added
ggplot2methods for automatically determining the +scale type of classesmoandab
- - Added names of object in the header in frequency tables, even when using pipes -
- Prevented
"bacteria"from getting coerced byas.ab()because Bacterial is a brand name of trimethoprim (TMP)
- - Fixed a bug where setting an antibiotic would not work for
eucast_rules()andmdro()+ - Added names of object in the header in frequency tables, even when +using pipes +
- Prevented
"bacteria"from getting coerced by +as.ab()because Bacterial is a brand name of trimethoprim +(TMP)
+ - Fixed a bug where setting an antibiotic would not work for
+
eucast_rules()andmdro()
- - Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin -
- Removed
latest_annual_releasefrom thecatalogue_of_life_version()function
- - Removed antibiotic code
PVM1from theantibioticsdata set as this was a duplicate ofPME+ - Fixed a EUCAST rule for Staphylococci, where amikacin resistance +would not be inferred from tobramycin +
- Removed
latest_annual_releasefrom the +catalogue_of_life_version()function
+ - Removed antibiotic code
PVM1from the +antibioticsdata set as this was a duplicate of +PME
- - Fixed bug where not all old taxonomic names would be printed, when using a vector as input for
as.mo()+ - Fixed bug where not all old taxonomic names would be printed, when
+using a vector as input for
as.mo()
- - Manually added Trichomonas vaginalis from the kingdom of Protozoa, which is missing from the Catalogue of Life -
- Small improvements to
plot()andbarplot()for MIC and RSI classes
- - Allow Catalogue of Life IDs to be coerced by
as.mo()+ - Manually added Trichomonas vaginalis from the kingdom of +Protozoa, which is missing from the Catalogue of Life +
- Small improvements to
plot()andbarplot()+for MIC and RSI classes
+ - Allow Catalogue of Life IDs to be coerced by
+
as.mo()
@@ -1215,77 +2003,124 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/@@ -1293,42 +2128,77 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/AMR 0.7.02019-06-03
New
-- Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use
as.rsi()on an MIC value (created withas.mic()), a disk diffusion value (created with the newas.disk()) or on a complete date set containing columns with MIC or disk diffusion values.
- - Function
mo_name()as alias ofmo_fullname()+- Support for translation of disk diffusion and MIC values to RSI
+values (i.e. antimicrobial interpretations). Supported guidelines are
+EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use
as.rsi()+on an MIC value (created withas.mic()), a disk diffusion +value (created with the newas.disk()) or on a complete +date set containing columns with MIC or disk diffusion values.
+ - Function
mo_name()as alias of +mo_fullname()
- - Added guidelines of the WHO to determine multi-drug resistance (MDR) for TB (
mdr_tb()) and added a new vignette about MDR. Read this tutorial here on our website.
+ - Added guidelines of the WHO to determine multi-drug resistance (MDR)
+for TB (
mdr_tb()) and added a new vignette about MDR. Read +this tutorial here on our +website.
- Support for translation of disk diffusion and MIC values to RSI
+values (i.e. antimicrobial interpretations). Supported guidelines are
+EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use
Changed
-- Fixed a critical bug in
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.
- - Fixed a bug in
eucast_rules()where antibiotics from WHONET software would not be recognised
+ - Fixed a critical bug in
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.
+ - Fixed a bug in
eucast_rules()where antibiotics from +WHONET software would not be recognised - Completely reworked the
antibioticsdata set:- All entries now have 3 different identifiers:
-
- Column
abcontains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package
- - Column
atccontains the ATC code, used by WHO/WHOCC
- - Column
cidcontains the CID code (Compound ID), used by PubChem
+ - Column
abcontains a human readable EARS-Net code, used +by ECDC and WHO/WHONET - this is the primary identifier used in this +package
+ - Column
atccontains the ATC code, used by +WHO/WHOCC
+ - Column
cidcontains the CID code (Compound ID), used by +PubChem
- - Column
- Based on the Compound ID, almost 5,000 official brand names have been added from many different countries -
- All references to antibiotics in our package now use EARS-Net codes, like
AMXfor amoxicillin
- - Functions
atc_certe,ab_umcgandatc_trivial_nlhave been removed
- - All
atc_*functions are superseded byab_*functions
- - All output will be translated by using an included translation file which can be viewed here +
- Based on the Compound ID, almost 5,000 official brand names have +been added from many different countries +
- All references to antibiotics in our package now use EARS-Net codes,
+like
AMXfor amoxicillin
+ - Functions
atc_certe,ab_umcgand +atc_trivial_nlhave been removed
+ - All
atc_*functions are superseded byab_*+functions
+ - All output will be translated by using an included translation file +which can +be viewed here
- All entries now have 3 different identifiers:
-
- Improvements to plotting AMR results with
ggplot_rsi():- New argument
coloursto set the bar colours
- - New arguments
title,subtitle,caption,x.titleandy.titleto set titles and axis descriptions
+ - New arguments
title,subtitle, +caption,x.titleandy.titleto +set titles and axis descriptions
- - New argument
- Improved intelligence of looking up antibiotic columns in a data set using
guess_ab_col()+ - Improved intelligence of looking up antibiotic columns in a data set
+using
guess_ab_col()
- - Added ~5,000 more old taxonomic names to the
microorganisms.olddata set, which leads to better results finding when using theas.mo()function
- - This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like
portion_df()andcount_df()this means that their new argumentcombine_SIis TRUE at default. Our plotting functionggplot_rsi()also reflects this change since it usescount_df()internally.
- - The
age()function gained a new argumentexactto determine ages with decimals
- - Removed deprecated functions
guess_mo(),guess_atc(),EUCAST_rules(),interpretive_reading(),rsi()+ - Added ~5,000 more old taxonomic names to the
+
microorganisms.olddata set, which leads to better results +finding when using theas.mo()function
+ - This package now honours the new EUCAST insight (2019) that S and I
+are but classified as susceptible, where I is defined as ‘increased
+exposure’ and not ‘intermediate’ anymore. For functions like
+
portion_df()andcount_df()this means that +their new argumentcombine_SIis TRUE at default. Our +plotting functionggplot_rsi()also reflects this change +since it usescount_df()internally.
+ - The
age()function gained a new argument +exactto determine ages with decimals
+ - Removed deprecated functions
guess_mo(), +guess_atc(),EUCAST_rules(), +interpretive_reading(),rsi()
- - Frequency tables (
freq()): + - Frequency tables (
freq()):speed improvement for microbial IDs
fixed factor level names for R Markdown
-when all values are unique it now shows a message instead of a warning
+when all values are unique it now shows a message instead of a +warning
-
support for boxplots:
- - Removed all hardcoded EUCAST rules and replaced them with a new reference file which can be viewed here +
- Removed all hardcoded EUCAST rules and replaced them with a new +reference file which can +be viewed here
- Added ceftazidim intrinsic resistance to Streptococci -
- Changed default settings for
age_groups(), to let groups of fives and tens end with 100+ instead of 120+
- - Fix for
freq()for when all values areNA+ - Changed default settings for
age_groups(), to let +groups of fives and tens end with 100+ instead of 120+
+ - Fix for
freq()for when all values are +NA - Fix for
first_isolate()for when dates are missing - Improved speed of
guess_ab_col()
- - Function
as.mo()now gently interprets any number of whitespace characters (like tabs) as one space
- - Function
as.mo()now returnsUNKNOWNfor"con"(WHONET ID of ‘contamination’) and returnsNAfor"xxx"(WHONET ID of ‘no growth’)
+ - Function
as.mo()now gently interprets any number of +whitespace characters (like tabs) as one space
+ - Function
as.mo()now returnsUNKNOWNfor +"con"(WHONET ID of ‘contamination’) and returns +NAfor"xxx"(WHONET ID of ‘no growth’) - Small algorithm fix for
as.mo()
- - Removed viruses from data set
microorganisms.codesand cleaned it up
- - Fix for
mo_shortname()where species would not be determined correctly
+ - Removed viruses from data set
microorganisms.codesand +cleaned it up
+ - Fix for
mo_shortname()where species would not be +determined correctly
Other
-- Support for R 3.6.0 and later by providing support for staged install
+
- Support for R 3.6.0 and later by providing support for staged +install
AMR 0.6.12019-03-29
Changed
-- Fixed a critical bug when using
eucast_rules()withverbose = TRUE+- Fixed a critical bug when using
eucast_rules()with +verbose = TRUE
- - Coercion of microbial IDs are now written to the package namespace instead of the user’s home folder, to comply with the CRAN policy +
- Coercion of microbial IDs are now written to the package namespace +instead of the user’s home folder, to comply with the CRAN policy
- Fixed a critical bug when using
- The
-
-
AMR 0.6.02019-03-27
New website!
-We’ve got a new website: https://msberends.gitlab.io/AMR (built with the great pkgdown)
- Contains the complete manual of this package and all of its functions with an explanation of their arguments -
- Contains a comprehensive tutorial about how to conduct AMR data analysis, import data from WHONET or SPSS and many more. +
- Contains the complete manual of this package and all of its +functions with an explanation of their arguments +
- Contains a comprehensive tutorial about how to conduct AMR data +analysis, import data from WHONET or SPSS and many more.
BREAKING: removed deprecated functions, arguments and references to ‘bactid’. Use
as.mo()to identify an MO code.
+BREAKING: removed deprecated functions, +arguments and references to ‘bactid’. Use
as.mo()to +identify an MO code.-
-
Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The
-microorganismsdata set now contains:All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa
-All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales (covering at least like all species of Aspergillus, Candida, Pneumocystis, Saccharomyces and Trichophyton)
-All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like Strongyloides and Taenia)
-All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed
+All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria +and Protozoa
+All ~3,000 (sub)species from these orders of the kingdom of +Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and +Schizosaccharomycetales (covering at least like all species of +Aspergillus, Candida, Pneumocystis, +Saccharomyces and Trichophyton)
+All ~2,000 (sub)species from ~100 other relevant genera, from the +kingdoms of Animalia and Plantae (like Strongyloides and +Taenia)
+All ~15,000 previously accepted names of included (sub)species +that have been taxonomically renamed
-
The responsible author(s) and year of scientific publication
-This data is updated annually - check the included version with the new function
+catalogue_of_life_version().This data is updated annually - check the included version with the +new function
catalogue_of_life_version().
- Due to this change, some
mocodes changed (e.g. Streptococcus changed fromB_STRPTCtoB_STRPT). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.
-New function
mo_rank()for the taxonomic rank (genus, species, infraspecies, etc.)
-New function
mo_url()to get the direct URL of a species from the Catalogue of Life
+Due to this change, some
mocodes changed +(e.g. Streptococcus changed fromB_STRPTCto +B_STRPT). A translation table is used internally to support +older microorganism IDs, so users will not notice this +difference.
+New function
mo_rank()for the taxonomic rank +(genus, species, infraspecies, etc.)
+New function
mo_url()to get the direct URL of a +species from the Catalogue of Life
Catalogue of Life as a new taxonomic source for data about +microorganisms, which also contains all ITIS data we used previously. +The
+microorganismsdata set now contains: -
-
Support for data from WHONET and EARS-Net (European Antimicrobial Resistance Surveillance Network):
-- Exported files from WHONET can be read and used in this package. For functions like
first_isolate()andeucast_rules(), all arguments will be filled in automatically.
- - This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the
antibioticsdata set now contains a columnears_net.
- - The function
as.mo()now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to themicroorganisms.codesdata set.
+ - Exported files from WHONET can be read and used in this package. For
+functions like
first_isolate()and +eucast_rules(), all arguments will be filled in +automatically.
+ - This package now knows all antibiotic abbrevations by EARS-Net
+(which are also being used by WHONET) - the
antibiotics+data set now contains a columnears_net.
+ - The function
as.mo()now knows all WHONET species +abbreviations too, because almost 2,000 microbial abbreviations were +added to themicroorganisms.codesdata set.
Support for data from WHONET +and EARS-Net +(European Antimicrobial Resistance Surveillance Network):
+ - Exported files from WHONET can be read and used in this package. For functions like
-
-
New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:
+New filters for antimicrobial classes. Use these functions to +filter isolates on results in one of more antibiotics from a specific +class:
-filter_aminoglycosides() @@ -1342,7 +2212,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ filter_glycopeptides() filter_macrolides() filter_tetracyclines()The
+antibioticsdata 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 theantibioticsdata set. For example:The
antibioticsdata 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 +antibioticsdata set. For example:septic_patients %>% filter_glycopeptides(result = "R") @@ -1351,7 +2224,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R -
-
All
+ab_*functions are deprecated and replaced byatc_*functions:All
ab_*functions are deprecated and replaced by +atc_*functions:-ab_property -> atc_property() @@ -1361,18 +2235,42 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ ab_certe -> atc_certe() ab_umcg -> atc_umcg() ab_tradenames -> atc_tradenames()These functions use
+as.atc()internally. The oldatc_propertyhas been renamedatc_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 classatcor must be coerable to this class. Properties of these classes should start with the same class name, analogous toas.mo()and e.g.mo_genus.These functions use
as.atc()internally. The old +atc_propertyhas 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 +atcor 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.
- New functions
set_mo_source()andget_mo_source()to use your own predefined MO codes as input foras.mo()and consequently allmo_*functions
-Support for the upcoming
dplyrversion 0.8.0
-New function
guess_ab_col()to find an antibiotic column in a table
-New function
mo_failures()to review values that could not be coerced to a valid MO code, usingas.mo(). This latter function will now only show a maximum of 10 uncoerced values and will refer tomo_failures().
-New function
mo_uncertainties()to review values that could be coerced to a valid MO code usingas.mo(), but with uncertainty.
-New function
mo_renamed()to get a list of all returned values fromas.mo()that have had taxonomic renaming
-New function
age()to calculate the (patients) age in years
-New function
age_groups()to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic AMR data analysis per age group.
+New functions
set_mo_source()and +get_mo_source()to use your own predefined MO codes as +input foras.mo()and consequently allmo_*+functions
+Support for the upcoming
dplyrversion +0.8.0
+New function
guess_ab_col()to find an antibiotic +column in a table
+New function
mo_failures()to review values that +could not be coerced to a valid MO code, usingas.mo(). +This latter function will now only show a maximum of 10 uncoerced values +and will refer tomo_failures().
+New function
mo_uncertainties()to review values +that could be coerced to a valid MO code usingas.mo(), but +with uncertainty.
+New function
mo_renamed()to get a list of all +returned values fromas.mo()that have had taxonomic +renaming
+New function
age()to calculate the (patients) age +in years
+New function
age_groups()to split ages into custom +or predefined groups (like children or elderly). This allows for easier +demographic AMR data analysis per age group.-
-
New function
+ggplot_rsi_predict()as well as the base Rplot()function can now be used for resistance prediction calculated withresistance_predict():New function
ggplot_rsi_predict()as well as the +base Rplot()function can now be used for resistance +prediction calculated withresistance_predict():x <- resistance_predict(septic_patients, col_ab = "amox") @@ -1380,7 +2278,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ ggplot_rsi_predict(x) -
-
Functions
+filter_first_isolate()andfilter_first_weighted_isolate()to shorten and fasten filtering on data sets with antimicrobial results, e.g.:Functions
filter_first_isolate()and +filter_first_weighted_isolate()to shorten and fasten +filtering on data sets with antimicrobial results, e.g.:septic_patients %>% filter_first_isolate(...) @@ -1394,26 +2294,50 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ filter(only_firsts == TRUE) %>% select(-only_firsts)
- New function
availability()to check the number of available (non-empty) results in adata.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.
+New function
availability()to check the number of +available (non-empty) results in adata.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.
- Function
eucast_rules(): -- Updated EUCAST Clinical breakpoints to version 9.0 of 1 January 2019, the data set
septic_patientsnow reflects these changes
- - Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately -
- Emphasised in manual that penicillin is meant as benzylpenicillin (ATC J01CE01) -
- New info is returned when running this function, stating exactly what has been changed or added. Use
eucast_rules(..., verbose = TRUE)to get a data set with all changed per bug and drug combination.
+ - Updated EUCAST Clinical breakpoints to version 9.0 of 1
+January 2019, the data set
septic_patientsnow reflects +these changes
+ - Fixed a critical bug where some rules that depend on previous +applied rules would not be applied adequately +
- Emphasised in manual that penicillin is meant as benzylpenicillin +(ATC J01CE01) +
- New info is returned when running this function, stating exactly
+what has been changed or added. Use
+
eucast_rules(..., verbose = TRUE)to get a data set with +all changed per bug and drug combination.
- - Updated EUCAST Clinical breakpoints to version 9.0 of 1 January 2019, the data set
- Removed data sets
microorganisms.oldDT,microorganisms.prevDT,microorganisms.unprevDTandmicroorganismsDTsince they were no longer needed and only contained info already available in themicroorganismsdata set
- - Added 65 antibiotics to the
antibioticsdata set, from the Pharmaceuticals Community Register of the European Commission
- - Removed columns
atc_group1_nlandatc_group2_nlfrom theantibioticsdata set
- - Functions
atc_ddd()andatc_groups()have been renamedatc_online_ddd()andatc_online_groups(). The old functions are deprecated and will be removed in a future version.
- - Function
guess_mo()is now deprecated in favour ofas.mo()and will be removed in future versions
- - Function
guess_atc()is now deprecated in favour ofas.atc()and will be removed in future versions
+ - Removed data sets
microorganisms.oldDT, +microorganisms.prevDT,microorganisms.unprevDT+andmicroorganismsDTsince they were no longer needed and +only contained info already available in themicroorganisms+data set
+ - Added 65 antibiotics to the
antibioticsdata set, from +the Pharmaceuticals +Community Register of the European Commission
+ - Removed columns
atc_group1_nland +atc_group2_nlfrom theantibioticsdata +set
+ - Functions
atc_ddd()andatc_groups()have +been renamedatc_online_ddd()and +atc_online_groups(). The old functions are deprecated and +will be removed in a future version.
+ - Function
guess_mo()is now deprecated in favour of +as.mo()and will be removed in future versions
+ - Function
guess_atc()is now deprecated in favour of +as.atc()and will be removed in future versions - Improvements for
as.mo():-
-
Now handles incorrect spelling, like
+iinstead ofyandfinstead ofph:Now handles incorrect spelling, like
iinstead of +yandfinstead ofph:# mo_fullname() uses as.mo() internally @@ -1425,7 +2349,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ #> [1] "Staphylococcus kloosii" -
-
Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default
+allow_uncertain = TRUEis equal to uncertainty level 2. Run?as.mofor more info about these levels.Uncertainty of the algorithm is now divided into four levels, 0 +to 3, where the default
allow_uncertain = TRUEis equal to +uncertainty level 2. Run?as.mofor more info about these +levels.-# equal: @@ -1435,84 +2362,135 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # also equal: as.mo(..., allow_uncertain = FALSE) as.mo(..., allow_uncertain = 0)Using
+as.mo(..., allow_uncertain = 3)could lead to very unreliable results.Using
as.mo(..., allow_uncertain = 3)could lead to very +unreliable results.
- Implemented the latest publication of Becker et al. (2019), for categorising coagulase-negative Staphylococci
-All microbial IDs that found are now saved to a local file
~/.Rhistory_mo. Use the new functionclean_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.
+Implemented the latest publication of Becker et al. +(2019), for categorising coagulase-negative +Staphylococci
+All microbial IDs that found are now saved to a local file +
~/.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.Fix for vector containing only empty values
Finds better results when input is in other languages
Better handling for subspecies
-Better handling for Salmonellae, especially the ‘city like’ serovars like Salmonella London
-Understanding of highly virulent E. coli strains like EIEC, EPEC and STEC
-There will be looked for uncertain results at default - these results will be returned with an informative warning
-Manual (help page) now contains more info about the algorithms
-Progress bar will be shown when it takes more than 3 seconds to get results
+Better handling for Salmonellae, especially the ‘city +like’ serovars like Salmonella London
+Understanding of highly virulent E. coli strains like +EIEC, EPEC and STEC
+There will be looked for uncertain results at default - these +results will be returned with an informative warning
+Manual (help page) now contains more info about the +algorithms
+Progress bar will be shown when it takes more than 3 seconds to +get results
Support for formatted console text
Console will return the percentage of uncoercable input
-
-
- Function
first_isolate(): -- Fixed a bug where distances between dates would not be calculated right - in the
septic_patientsdata set this yielded a difference of 0.15% more isolates
- - Will now use a column named like “patid” for the patient ID (argument
col_patientid), when this argument was left blank
- - Will now use a column named like “key(…)ab” or “key(…)antibiotics” for the key antibiotics (argument
col_keyantibiotics()), when this argument was left blank
- - Removed argument
output_logical, the function will now always return a logical value
- - Renamed argument
filter_specimentospecimen_group, although usingfilter_specimenwill still work
+ - Fixed a bug where distances between dates would not be calculated
+right - in the
septic_patientsdata set this yielded a +difference of 0.15% more isolates
+ - Will now use a column named like “patid” for the patient ID
+(argument
col_patientid), when this argument was left +blank
+ - Will now use a column named like “key(…)ab” or “key(…)antibiotics”
+for the key antibiotics (argument
col_keyantibiotics()), +when this argument was left blank
+ - Removed argument
output_logical, the function will now +always return a logical value
+ - Renamed argument
filter_specimento +specimen_group, although usingfilter_specimen+will still work
- - Fixed a bug where distances between dates would not be calculated right - in the
- A note to the manual pages of the
portionfunctions, that low counts can influence the outcome and that theportionfunctions may camouflage this, since they only return the portion (albeit being dependent on theminimumargument)
- - Merged data sets
microorganisms.certeandmicroorganisms.umcgintomicroorganisms.codes+ - A note to the manual pages of the
portionfunctions, +that low counts can influence the outcome and that the +portionfunctions may camouflage this, since they only +return the portion (albeit being dependent on theminimum+argument)
+ - Merged data sets
microorganisms.certeand +microorganisms.umcginto +microorganisms.codes
- - Function
mo_taxonomy()now contains the kingdom too
- - Reduce false positives for
is.rsi.eligible()using the newthresholdargument
+ - Function
mo_taxonomy()now contains the kingdom +too
+ - Reduce false positives for
is.rsi.eligible()using the +newthresholdargument - New colours for
scale_rsi_colours()
- - Summaries of class
mowill now return the top 3 and the unique count, e.g. usingsummary(mo)+ - Summaries of class
mowill now return the top 3 and the +unique count, e.g. usingsummary(mo)
- - Small text updates to summaries of class
rsiandmic+ - Small text updates to summaries of class
rsiand +mic - Function
as.rsi():- Now gives a warning when inputting MIC values -
- Now accepts high and low resistance:
"HIGH S"will returnS+ - Now accepts high and low resistance:
"HIGH S"will +returnS
- - Frequency tables (
freq()function): + - Frequency tables (
freq()function):-
-
Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:
+Support for tidyverse quasiquotation! Now you can create +frequency tables of function outcomes:
+ 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) + 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
headerfunction
-The argument
headeris now set toTRUEat default, even for markdown
-Added header info for class
moto show unique count of families, genera and species
-Now honours the
decimal.marksetting, which just likeformatdefaults togetOption("OutDec")
-The new
big.markargument will at default be","whendecimal.mark = "."and"."otherwise
-Fix for header text where all observations are
NA
-New argument
droplevelsto exclude empty factor levels when input is a factor
-Factor levels will be in header when present in input data (maximum of 5)
+Header info is now available as a list, with the +
headerfunction
+The argument
headeris now set toTRUE+at default, even for markdown
+Added header info for class
moto show unique count +of families, genera and species
+Now honours the
decimal.marksetting, which just +likeformatdefaults to +getOption("OutDec")
+The new
big.markargument will at default be +","whendecimal.mark = "."and +"."otherwise
+Fix for header text where all observations are +
NA
+New argument
droplevelsto exclude empty factor +levels when input is a factor
+Factor levels will be in header when present in input data +(maximum of 5)
Fix for using
select()on frequency tables
We’ve got a new website: https://msberends.gitlab.io/AMR
+(built with the great pkgdown)
New
-Changed
scale_y_percent() now contains the limits argumentmdro(), key_antibiotics() and eucast_rules()
+scale_y_percent() now contains the
+limits argumentmdro(),
+key_antibiotics() and eucast_rules()
resistance_predict() function)as.mic() to support more values ending in (several) zeroes%like%, it will now return the callresistance_predict() function)as.mic() to support more values ending in
+(several) zeroes%like%,
+it will now return the callNew
- Repository moved to GitLab -
- Function
count_allto get all available isolates (that like allportion_*andcount_*functions also supportssummariseandgroup_by), the oldn_rsiis now an alias ofcount_all+ - Function
count_allto get all available isolates (that +like allportion_*andcount_*functions also +supportssummariseandgroup_by), the old +n_rsiis now an alias ofcount_all
- - Function
get_localeto determine language for language-dependent output for somemo_*functions. This is now the default value for theirlanguageargument, by which the system language will be used at default.
- - Data sets
microorganismsDT,microorganisms.prevDT,microorganisms.unprevDTandmicroorganisms.oldDTto improve the speed ofas.mo. They are for reference only, since they are primarily for internal use ofas.mo.
- - Function
read.4Dto read from the 4D database of the MMB department of the UMCG
- - Functions
mo_authorsandmo_yearto get specific values about the scientific reference of a taxonomic entry
+ - Function
get_localeto determine language for +language-dependent output for somemo_*functions. This is +now the default value for theirlanguageargument, by which +the system language will be used at default.
+ - Data sets
microorganismsDT, +microorganisms.prevDT,microorganisms.unprevDT+andmicroorganisms.oldDTto improve the speed of +as.mo. They are for reference only, since they are +primarily for internal use ofas.mo.
+ - Function
read.4Dto read from the 4D database of the +MMB department of the UMCG
+ - Functions
mo_authorsandmo_yearto get +specific values about the scientific reference of a taxonomic entry
Changed
-Functions
MDRO,BRMO,MRGNandEUCAST_exceptional_phenotypeswere renamed tomdro,brmo,mrgnandeucast_exceptional_phenotypes
-EUCAST_ruleswas renamed toeucast_rules, the old function still exists as a deprecated function
+Functions
MDRO,BRMO,MRGN+andEUCAST_exceptional_phenotypeswere renamed to +mdro,brmo,mrgnand +eucast_exceptional_phenotypes
+EUCAST_ruleswas renamed to +eucast_rules, the old function still exists as a deprecated +function-
Big changes to the
-eucast_rulesfunction:- Now also applies rules from the EUCAST ‘Breakpoint tables for bacteria’, version 8.1, 2018, https://www.eucast.org/clinical_breakpoints/ (see Source of the function) -
- New argument
rulesto specify which rules should be applied (expert rules, breakpoints, others or all)
- - New argument
verbosewhich can be set toTRUEto get very specific messages about which columns and rows were affected
- - Better error handling when rules cannot be applied (i.e. new values could not be inserted) -
- The number of affected values will now only be measured once per row/column combination -
- Data set
septic_patientsnow reflects these changes
- - Added argument
pipefor piperacillin (J01CA12), also to themdrofunction
+ - Now also applies rules from the EUCAST ‘Breakpoint tables for +bacteria’, version 8.1, 2018, https://www.eucast.org/clinical_breakpoints/ (see Source +of the function) +
- New argument
rulesto specify which rules should be +applied (expert rules, breakpoints, others or all)
+ - New argument
verbosewhich can be set to +TRUEto get very specific messages about which columns and +rows were affected
+ - Better error handling when rules cannot be applied (i.e. new values +could not be inserted) +
- The number of affected values will now only be measured once per +row/column combination +
- Data set
septic_patientsnow reflects these +changes
+ - Added argument
pipefor piperacillin (J01CA12), also to +themdrofunction - Small fixes to EUCAST clinical breakpoint rules
- Added column
kingdomto the microorganisms data set, and functionmo_kingdomto look up values
-Tremendous speed improvement for
as.mo(and subsequently allmo_*functions), as empty values wil be ignored a priori
-Fewer than 3 characters as input for
as.mowill return NA
+Added column
kingdomto the microorganisms data set, +and functionmo_kingdomto look up values
+Tremendous speed improvement for
as.mo(and +subsequently allmo_*functions), as empty values wil be +ignored a priori
+Fewer than 3 characters as input for
as.mowill +return NA-
-
Function
+as.mo(and allmo_*wrappers) now supports genus abbreviations with “species” attachedFunction
as.mo(and allmo_*wrappers) +now supports genus abbreviations with “species” attachedas.mo("E. species") # B_ESCHR @@ -1554,45 +2563,69 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ as.mo("S. spp") # B_STPHY mo_fullname("S. species") # "Staphylococcus species"
- Added argument
combine_IR(TRUE/FALSE) to functionsportion_dfandcount_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
-Added argument
also_single_testedforportion_*andcount_*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
-Using
portion_*functions now throws a warning when total available isolate is below argumentminimum
-Functions
as.mo,as.rsi,as.mic,as.atcandfreqwill not set package name as attribute anymore
+Added argument
combine_IR(TRUE/FALSE) to functions +portion_dfandcount_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
+Added argument
also_single_testedfor +portion_*andcount_*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
+Using
portion_*functions now throws a warning when +total available isolate is below argumentminimum
+Functions
as.mo,as.rsi, +as.mic,as.atcandfreqwill not +set package name as attribute anymore-
-
Frequency tables -
+freq():Frequency tables -
freq():-
Support for grouping variables, test with:
+ freq(gender)
-
Support for (un)selecting columns:
Check for hms::is.hms
Now prints in markdown at default in non-interactive sessions
No longer adds the factor level column and sorts factors on count again
Now prints in markdown at default in non-interactive +sessions
No longer adds the factor level column and sorts factors on count +again
Support for class difftime
New argument na, to choose which character to print for empty values
New argument header to turn the header info off (default when markdown = TRUE)
New argument title to manually setbthe title of the frequency table
New argument na, to choose which character to print
+for empty values
New argument header to turn the header info off
+(default when markdown = TRUE)
New argument title to manually setbthe title of the
+frequency table
first_isolate now tries to find columns to use as input when arguments are left blank
Improvements for MDRO algorithm (function mdro)
Data set septic_patients is now a data.frame, not a tibble anymore
Removed diacritics from all authors (columns microorganisms$ref and microorganisms.old$ref) to comply with CRAN policy to only allow ASCII characters
first_isolate now tries to find columns to use as
+input when arguments are left blank
Improvements for MDRO algorithm (function
+mdro)
Data set septic_patients is now a
+data.frame, not a tibble anymore
Removed diacritics from all authors (columns
+microorganisms$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()
ggplot_rsi and scale_y_percent have breaks argument
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()
ggplot_rsi and scale_y_percent have
+breaks argument
AI improvements for as.mo:
- @@ -1609,16 +2642,24 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
Fix for join functions
Speed improvement for is.rsi.eligible, now 15-20 times faster
In g.test, when sum(x) is below 1000 or any of the expected values is below 5, Fisher’s Exact Test will be suggested
ab_name will try to fall back on as.atc when no results are found
Speed improvement for is.rsi.eligible, now 15-20
+times faster
In g.test, when sum(x) is below 1000 or
+any of the expected values is below 5, Fisher’s Exact Test will be
+suggested
ab_name will try to fall back on as.atc
+when no results are found
Removed the addin to view data sets
Percentages will now will rounded more logically (e.g. in freq function)
Percentages will now will rounded more logically (e.g. in
+freq function)
Other
-- New dependency on package
crayon, to support formatted text in the console
- - Dependency
tidyris now mandatory (went toImportfield) sinceportion_dfandcount_dfrely on it
+ - New dependency on package
crayon, to support formatted +text in the console
+ - Dependency
tidyris now mandatory (went to +Importfield) sinceportion_dfand +count_dfrely on it - Updated vignettes to comply with README
AMR 0.4.02018-10-01
New
-The data set
microorganismsnow 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 setmicroorganisms.oldcontains all previously known taxonomic names from those kingdoms.
+The data set
microorganismsnow 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 +setmicroorganisms.oldcontains all previously known +taxonomic names from those kingdoms.-
-
New functions based on the existing function
-mo_property:- Taxonomic names:
mo_phylum,mo_class,mo_order,mo_family,mo_genus,mo_species,mo_subspecies+New functions based on the existing function +
+mo_property:- Taxonomic names:
mo_phylum,mo_class, +mo_order,mo_family,mo_genus, +mo_species,mo_subspecies
- - Semantic names:
mo_fullname,mo_shortname+ - Semantic names:
mo_fullname, +mo_shortname
- - Microbial properties:
mo_type,mo_gramstain+ - Microbial properties:
mo_type, +mo_gramstain - Author and year:
mo_ref
-
They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
+ - Taxonomic names:
They also come with support for German, Dutch, French, Italian, +Spanish and Portuguese:
-mo_gramstain("E. coli") @@ -1648,7 +2703,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # [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:
+Furthermore, former taxonomic names will give a note about the +current taxonomic name:
mo_gramstain("Esc blattae") @@ -1656,12 +2712,24 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # [1] "Gram negative" - Taxonomic names:
-
-
Functions
-count_R,count_IR,count_I,count_SIandcount_Sto selectively count resistant or susceptible isolates- Extra function
count_df(which works likeportion_df) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables
+ - Extra function
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 variables
Functions
+count_R,count_IR, +count_I,count_SIandcount_Sto +selectively count resistant or susceptible isolates
- - Extra function
Function
is.rsi.eligibleto check for columns that have valid antimicrobial results, but do not have thersiclass yet. Transform the columns of your raw data with:data %>% mutate_if(is.rsi.eligible, as.rsi)
+Function
is.rsi.eligibleto check for columns that +have valid antimicrobial results, but do not have thersi+class yet. Transform the columns of your raw data with: +data %>% mutate_if(is.rsi.eligible, as.rsi)-
-
Functions
+as.moandis.moas replacements foras.bactidandis.bactid(since themicrooganismsdata set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. Theas.mofunction determines microbial IDs using intelligent rules:Functions
as.moandis.moas +replacements foras.bactidandis.bactid+(since themicrooganismsdata set not only contains +bacteria). These last two functions are deprecated and will be removed +in a future release. Theas.mofunction determines +microbial IDs using intelligent rules:-as.mo("E. coli") @@ -1670,7 +2738,8 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # [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:
+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:
thousands_of_E_colis <- rep("E. coli", 25000) @@ -1679,27 +2748,44 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/ # min median max neval # 0.01817717 0.01843957 0.03878077 100
- Added argument
reference_dfforas.mo, so users can supply their own microbial IDs, name or codes as a reference table
+Added argument
reference_dfforas.mo, +so users can supply their own microbial IDs, name or codes as a +reference table-
-
Renamed all previous references to
-bactidtomo, like:- Column names inputs of
EUCAST_rules,first_isolateandkey_antibiotics+Renamed all previous references to
+bactidto +mo, like:- Column names inputs of
EUCAST_rules, +first_isolateandkey_antibiotics
- - Column names of datasets
microorganismsandseptic_patients+ - Column names of datasets
microorganismsand +septic_patients
- - All old syntaxes will still work with this version, but will throw warnings +
- All old syntaxes will still work with this version, but will throw +warnings
- - Column names inputs of
Function
labels_rsi_countto print datalabels on a RSIggplot2model
-Functions
as.atcandis.atcto transform/look up antibiotic ATC codes as defined by the WHO. The existing functionguess_atcis now an alias ofas.atc.
-Function
ab_propertyand its aliases:ab_name,ab_tradenames,ab_certe,ab_umcgandab_trivial_nl
+Function
labels_rsi_countto print datalabels on a +RSIggplot2model
+Functions
as.atcandis.atcto +transform/look up antibiotic ATC codes as defined by the WHO. The +existing functionguess_atcis now an alias of +as.atc.
+Function
ab_propertyand its aliases: +ab_name,ab_tradenames,ab_certe, +ab_umcgandab_trivial_nlIntroduction to AMR as a vignette
-Removed clipboard functions as it violated the CRAN policy
-Renamed
septic_patients$sextoseptic_patients$gender
+Removed clipboard functions as it violated the CRAN +policy
+Renamed
septic_patients$sexto +septic_patients$gender
- Column names inputs of
Changed
-Added three antimicrobial agents to the
antibioticsdata set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
+Added three antimicrobial agents to the
antibiotics+data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole +(D01AC05)-
-
Added 163 trade names to the
+antibioticsdata set, it now contains 298 different trade names in total, e.g.:Added 163 trade names to the
antibioticsdata 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
ratiois now deprecated and will be removed in a future release, as it is not really the scope of this package
-Fix for
as.micfor values ending in zeroes after a real number
-Small fix where B. fragilis would not be found in the
microorganisms.umcgdata set
-Added
prevalencecolumn to themicroorganismsdata set
-Added arguments
minimumandas_percenttoportion_df
+For
first_isolate, rows will be ignored when there’s +no species available
+Function
ratiois now deprecated and will be removed +in a future release, as it is not really the scope of this +package
+Fix for
as.micfor values ending in zeroes after a +real number
+Small fix where B. fragilis would not be found in the +
microorganisms.umcgdata set
+Added
prevalencecolumn to the +microorganismsdata set
+Added arguments
minimumandas_percent+toportion_df-
-
Support for quasiquotation in the functions series
+count_*andportions_*, andn_rsi. This allows to check for more than 2 vectors or columns.Support for quasiquotation in the functions series +
count_*andportions_*, and +n_rsi. This allows to check for more than 2 vectors or +columns.
- Edited
ggplot_rsiandgeom_rsiso they can cope withcount_df. The newfunargument has valueportion_dfat default, but can be set tocount_df.
-Fix for
ggplot_rsiwhen theggplot2package was not loaded
-Added datalabels function
labels_rsi_counttoggplot_rsi
-Added possibility to set any argument to
geom_rsi(andggplot_rsi) so you can set your own preferences
-Fix for joins, where predefined suffices would not be honoured
-Added argument
quoteto thefreqfunction
-Added generic function
difffor frequency tables
-Added longest en shortest character length in the frequency table (
freq) header of classcharacter
+Edited
ggplot_rsiandgeom_rsiso they +can cope withcount_df. The newfunargument +has valueportion_dfat default, but can be set to +count_df.
+Fix for
ggplot_rsiwhen theggplot2+package was not loaded
+Added datalabels function
labels_rsi_countto +ggplot_rsi
+Added possibility to set any argument to
geom_rsi+(andggplot_rsi) so you can set your own +preferences
+Fix for joins, where predefined suffices would not be +honoured
+Added argument
quoteto thefreq+function
+Added generic function
difffor frequency +tables
+Added longest en shortest character length in the frequency table +(
freq) header of classcharacter-
-
Support for types (classes) list and matrix for
+freqSupport for types (classes) list and matrix for +
+freq(my_matrix)freq
For lists, subsetting is possible:
my_list = list(age = septic_patients$age, gender = septic_patients$gender)
-my_list %>% freq(age)
-my_list %>% freq(gender)New
-
-BREAKING:
rsi_dfwas removed in favour of new functionsportion_R,portion_IR,portion_I,portion_SIandportion_Sto selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the oldrsifunction. The old function still works, but is deprecated. -- New function
portion_dfto get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables
+BREAKING: - New function
portion_dfto get all portions of S, I and +R of a data set with antibiotic columns, with support for grouped +variables
rsi_dfwas removed in favour +of new functionsportion_R,portion_IR, +portion_I,portion_SIand +portion_Sto selectively calculate resistance or +susceptibility. These functions are 20 to 30 times faster than the old +rsifunction. The old function still works, but is +deprecated. + - New function
-
-BREAKING: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call key antibiotics) to include more first isolates (afterwards called first weighted isolates) are now as follows:
-
- Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole -
- Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin -
- Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem +BREAKING: the methodology for determining first +weighted isolates was changed. The antibiotics that are compared between +isolates (call key antibiotics) to include more first isolates +(afterwards called first weighted isolates) are now as follows: +
- Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, +piperacillin/tazobactam, ciprofloxacin, +trimethoprim/sulfamethoxazole +
- Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, +oxacillin, rifampicin +
- Gram-negative: gentamicin, tobramycin, colistin, cefotaxime, +ceftazidime, meropenem
- Support for
ggplot2-- New functions
geom_rsi,facet_rsi,scale_y_percent,scale_rsi_coloursandtheme_rsi+- New functions
geom_rsi,facet_rsi, +scale_y_percent,scale_rsi_coloursand +theme_rsi
- - New wrapper function
ggplot_rsito apply all above functions on a data set: + - New wrapper function
ggplot_rsito apply all above +functions on a data set:-
-
septic_patients %>% select(tobr, gent) %>% ggplot_rsiwill show portions of S, I and R immediately in a pretty plot
+
septic_patients %>% select(tobr, gent) %>% ggplot_rsi+will show portions of S, I and R immediately in a pretty plot -
-
- Support for grouped variables, see
?ggplot_rsi
- New functions
- New functions
- Determining bacterial ID:
-
- New functions
as.bactidandis.bactidto transform/ look up microbial ID’s.
- - The existing function
guess_bactidis now an alias ofas.bactid+- New functions
as.bactidandis.bactidto +transform/ look up microbial ID’s.
+ - The existing function
guess_bactidis now an alias of +as.bactid
- - New Becker classification for Staphylococcus to categorise them into Coagulase Negative Staphylococci (CoNS) and Coagulase Positve Staphylococci (CoPS) -
- New Lancefield classification for Streptococcus to categorise them into Lancefield groups +
- New Becker classification for Staphylococcus to categorise +them into Coagulase Negative Staphylococci (CoNS) and Coagulase +Positve Staphylococci (CoPS) +
- New Lancefield classification for Streptococcus to +categorise them into Lancefield groups
- - New functions
- For convience, new descriptive statistical functions
kurtosisandskewnessthat are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
- - Function
g.testto perform the X2 distributed G-test, which use is the same aschisq.test+ - For convience, new descriptive statistical functions
+
kurtosisandskewnessthat are lacking in base +R - they are generic functions and have support for vectors, data.frames +and matrices
+ - Function
g.testto perform the X2 +distributed G-test, which +use is the same aschisq.test -
-
Function-ratioto transform a vector of values to a preset ratioFor example:ratio(c(10, 500, 10), ratio = "1:2:1")would return130, 260, 130
+For example: +ratio(c(10, 500, 10), ratio = "1:2:1")would return +130, 260, 130
Function+ratioto transform a vector of values to +a preset ratio
- - 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
- - Function
p.symbolto transform p values to their related symbols:0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1+ - 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
+ - Function
p.symbolto transform p values to their +related symbols: +0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
- - Functions
clipboard_importandclipboard_exportas helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use thecliprpackage, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)
+ - Functions
clipboard_importand +clipboard_exportas helper functions to quickly copy and +paste from/to software like Excel and SPSS. These functions use the +cliprpackage, but are a little altered to also support +headless Linux servers (so you can use it in RStudio Server) - New for frequency tables (function
freq):- A vignette to explain its usage -
- Support for
rsi(antimicrobial resistance) to use as input
- - Support for
tableto use as input:freq(table(x, y))+ - Support for
rsi(antimicrobial resistance) to use as +input
+ - Support for
tableto use as input: +freq(table(x, y))
- - Support for existing functions
histandplotto use a frequency table as input:hist(freq(df$age))+ - Support for existing functions
histand +plotto use a frequency table as input: +hist(freq(df$age))
- - Support for
as.vector,as.data.frame,as_tibbleandformat+ - Support for
as.vector,as.data.frame, +as_tibbleandformat
- - Support for quasiquotation:
freq(mydata, mycolumn)is the same asmydata %>% freq(mycolumn)+ - Support for quasiquotation:
freq(mydata, mycolumn)is +the same asmydata %>% freq(mycolumn)
- - Function
top_freqfunction to return the top/below n items as vector
- - Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR) -
- Possibility to globally set the default for the amount of items to print, with
options(max.print.freq = n)where n is your preset value
+ - Function
top_freqfunction to return the top/below +n items as vector
+ - Header of frequency tables now also show Mean Absolute Deviaton +(MAD) and Interquartile Range (IQR) +
- Possibility to globally set the default for the amount of items to
+print, with
options(max.print.freq = n)where n is +your preset value
- New functions
Changed
-- Improvements for forecasting with
resistance_predictand added more examples
+ - Improvements for forecasting with
resistance_predict+and added more examples - More antibiotics added as arguments for EUCAST rules -
- Updated version of the
septic_patientsdata set to better reflect the reality
- - Pretty printing for tibbles removed as it is not really the scope of this package -
- Printing of
micandrsiclasses now returns all values - usefreqto check distributions
- - Improved speed of key antibiotics comparison for determining first isolates -
- Column names for the
key_antibioticsfunction are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs
+ - Updated version of the
septic_patientsdata set to +better reflect the reality
+ - Pretty printing for tibbles removed as it is not really the scope of +this package +
- Printing of
micandrsiclasses now +returns all values - usefreqto check distributions
+ - Improved speed of key antibiotics comparison for determining first +isolates +
- Column names for the
key_antibioticsfunction are now +generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for +Gram-negative specific ABs - Speed improvement for the
abnamefunction -
%like%now supports multiple patterns
- - Frequency tables are now actual
data.frames with altered console printing to make it look like a frequency table. Because of this, the argumenttoConsoleis not longer needed.
- - Fix for
freqwhere the class of an item would be lost
- - Small translational improvements to the
septic_patientsdataset and the columnbactidnow has the new class"bactid"+ - Frequency tables are now actual
data.frames with +altered console printing to make it look like a frequency table. Because +of this, the argumenttoConsoleis not longer needed.
+ - Fix for
freqwhere the class of an item would be +lost
+ - Small translational improvements to the
septic_patients+dataset and the columnbactidnow has the new class +"bactid"
- - Small improvements to the
microorganismsdataset (especially for Salmonella) and the columnbactidnow has the new class"bactid"+ - Small improvements to the
microorganismsdataset +(especially for Salmonella) and the columnbactid+now has the new class"bactid"
- - Combined MIC/RSI values will now be coerced by the
rsiandmicfunctions: + - Combined MIC/RSI values will now be coerced by the
rsi+andmicfunctions:-
as.rsi("<=0.002; S")will returnS -
-
as.mic("<=0.002; S")will return<=0.002+as.mic("<=0.002; S")will return +<=0.002
- -
- Now possible to coerce MIC values with a space between operator and value, i.e.
as.mic("<= 0.002")now works
- - Classes
rsiandmicdo not add the attributepackage.versionanymore
- - Added
"groups"option foratc_property(..., property). It will return a vector of the ATC hierarchy as defined by the WHO. The new functionatc_groupsis a convenient wrapper around this.
- - Build-in host check for
atc_propertyas it requires the host set byurlto be responsive
- - Improved
first_isolatealgorithm to exclude isolates where bacteria ID or genus is unavailable
- - Fix for warning hybrid evaluation forced for row_number (
924b62) from thedplyrpackage v0.7.5 and above
- - Support for empty values and for 1 or 2 columns as input for
guess_bactid(now calledas.bactid) -- So
yourdata %>% select(genus, species) %>% as.bactid()now also works
+ - Now possible to coerce MIC values with a space between operator and
+value, i.e.
as.mic("<= 0.002")now works
+ - Classes
rsiandmicdo not add the +attributepackage.versionanymore
+ - Added
"groups"option for +atc_property(..., property). It will return a vector of the +ATC hierarchy as defined by the WHO. The +new functionatc_groupsis a convenient wrapper around +this.
+ - Build-in host check for
atc_propertyas it requires the +host set byurlto be responsive
+ - Improved
first_isolatealgorithm to exclude isolates +where bacteria ID or genus is unavailable
+ - Fix for warning hybrid evaluation forced for row_number (
924b62) +from thedplyrpackage v0.7.5 and above
+ - Support for empty values and for 1 or 2 columns as input for
+
guess_bactid(now calledas.bactid) +- So
+
yourdata %>% select(genus, species) %>% as.bactid()+now also works
- So
+
- Other small fixes
- So
Other
-- Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
+
- Added integration tests (check if everything works as expected) for
+all releases of R 3.1 and higher
- Linux and macOS: https://travis-ci.org/msberends/AMR
- Windows: https://ci.appveyor.com/project/msberends/amr
@@ -1865,41 +3052,66 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
New
- Full support for Windows, Linux and macOS -
- Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies) -
- Function
n_rsito count cases where antibiotic test results were available, to be used in conjunction withdplyr::summarise, see ?rsi
- - Function
guess_bactidto determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
- - Function
guess_atcto determine the ATC of an antibiotic based on name, trade name, or known abbreviations
- - Function
freqto create frequency tables, with additional info in a header
- - Function
MDROto determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. + - Full support for old R versions, only R-3.0.0 (April 2013) or later +is needed (needed packages may have other dependencies) +
- Function
n_rsito count cases where antibiotic test +results were available, to be used in conjunction with +dplyr::summarise, see ?rsi
+ - Function
guess_bactidto determine the +ID of a microorganism based on genus/species or known +abbreviations like MRSA
+ - Function
guess_atcto determine the +ATC of an antibiotic based on name, trade name, or known +abbreviations
+ - Function
freqto create frequency +tables, with additional info in a header
+ - Function
MDROto determine Multi Drug Resistant +Organisms (MDRO) with support for country-specific guidelines.- -Exceptional resistances defined by EUCAST are also supported instead of countries alone -
- Functions
BRMOandMRGNare wrappers for Dutch and German guidelines, respectively
+Exceptional
+resistances defined by EUCAST are also supported instead of
+countries alone
+ - Functions
BRMOandMRGNare wrappers for +Dutch and German guidelines, respectively
- New algorithm to determine weighted isolates, can now be
"points"or"keyantibiotics", see?first_isolate+- New algorithm to determine weighted isolates, can now be +
-"points"or"keyantibiotics", see +?first_isolate- New print format for
+tibbles anddata.tables- New print format for
tibbles and +data.tablesChanged
-- Fixed
rsiclass for vectors that contain only invalid antimicrobial interpretations
+ - Fixed
rsiclass for vectors that contain only invalid +antimicrobial interpretations - Renamed dataset
ablisttoantibiotics
- - Renamed dataset
bactlisttomicroorganisms+ - Renamed dataset
bactlistto +microorganisms
- - Added common abbreviations and trade names to the
antibioticsdataset
- - Added more microorganisms to the
microorganismsdataset
- - Added analysis examples on help page of dataset
septic_patients+ - Added common abbreviations and trade names to the
+
antibioticsdataset
+ - Added more microorganisms to the
microorganisms+dataset
+ - Added analysis examples on help page of dataset
+
septic_patients
- - Added support for character vector in
joinfunctions
- - Added warnings when a join results in more rows after than before the join +
- Added support for character vector in
join+functions
+ - Added warnings when a join results in more rows after than before +the join
- Altered
%like%to make it case insensitive
- - For arguments of functions
first_isolateandEUCAST_rulescolumn names are now case-insensitive
- - Functions
as.rsiandas.micnow add the package name and version as attributes
+ - For arguments of functions
first_isolateand +EUCAST_rulescolumn names are now case-insensitive
+ - Functions
as.rsiandas.micnow add the +package name and version as attributes
@@ -184,11 +184,13 @@ The lifecycle of this function is retiredOther
- Expanded
README.mdwith more examples
- - Added ORCID of authors to DESCRIPTION file +
- Added ORCID of authors to +DESCRIPTION file
- Added unit testing with the
testthatpackage - Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
- Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/main/R) @@ -1908,11 +3120,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
-
-
EUCAST_rulesapplies for amoxicillin even if ampicillin is missing
- - Edited column names to comply with GLIMS, the laboratory information system +
- Edited column names to comply with GLIMS, the laboratory information +system
- Added more valid MIC values
- Renamed ‘Daily Defined Dose’ to ‘Defined Daily Dose’ -
- Added barplots for
rsiandmicclasses
+ - Added barplots for
rsiandmic+classes
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index eac16ae7..84783e52 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ -pandoc: 2.14.0.3 -pkgdown: 2.0.0 +pandoc: 2.17.1.1 +pkgdown: 2.0.2 pkgdown_sha: ~ articles: AMR: AMR.html @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-12-23T17:53Z +last_built: 2022-03-14T15:33Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 8b30fd9e..bd86fc68 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -17,7 +17,7 @@AMR 0.1.12018-03-14
EUCAST_rulesapplies for amoxicillin even if ampicillin +is missing +-Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.
+Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, +Erwin E. A. Hassing.
- Added integration tests (check if everything works as expected) for
+all releases of R 3.1 and higher
Welcome to the AMR package.
Details
@@ -222,11 +221,13 @@ The NetherlandsThis example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antibiotic results are from our example_isolates data set. All patient names are created using online surname generators and are only in place for practice purposes.
WHONETWHONETFormat
@@ -213,11 +215,13 @@as.mo() to use the data for intel
diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html
index 0adbedb7..a06ce87b 100644
--- a/docs/reference/catalogue_of_life_version.html
+++ b/docs/reference/catalogue_of_life_version.html
@@ -17,7 +17,7 @@
@@ -200,11 +200,13 @@ This package contains the complete taxonomic tree of almost all microorganisms (
diff --git a/docs/reference/count.html b/docs/reference/count.html
index d35f444e..9c6a5887 100644
--- a/docs/reference/count.html
+++ b/docs/reference/count.html
@@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html
index 8b973fa8..eb4bc8cd 100644
--- a/docs/reference/custom_eucast_rules.html
+++ b/docs/reference/custom_eucast_rules.html
@@ -17,7 +17,7 @@
diff --git a/docs/reference/dosage.html b/docs/reference/dosage.html
index 84972a57..f5a67eff 100644
--- a/docs/reference/dosage.html
+++ b/docs/reference/dosage.html
@@ -17,7 +17,7 @@
@@ -161,7 +161,9 @@
EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with eucast_dosage().
dosagedosageFormat
@@ -200,11 +202,13 @@A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR data analysis. For examples, please read the tutorial on our website.
-example_isolatesexample_isolatesFormat
@@ -197,11 +199,13 @@A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.
-example_isolates_uncleanexample_isolates_uncleanFormat
@@ -192,11 +194,13 @@Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
-intrinsic_resistantintrinsic_resistantFormat
@@ -208,11 +210,13 @@Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use as.rsi() to transform MICs or disks measurements to R/SI values.
rsi_translationrsi_translation