@@ -260,21 +260,21 @@ make the structure of your data generally look like this:
-
2024-02-13
+
2024-02-24
abcd
Escherichia coli
S
S
-
2024-02-13
+
2024-02-24
abcd
Escherichia coli
S
R
-
2024-02-13
+
2024-02-24
efgh
Escherichia coli
R
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 6ffe8021..fd53d150 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -38,7 +38,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/articles/MDR.html b/articles/MDR.html
index 85fc39f5..c4f19094 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -38,7 +38,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
@@ -401,19 +401,19 @@ names or codes, this would have worked exactly the same way:
head(my_TB_data)#> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-#> 1 S R S S S S
-#> 2 R S S S I I
-#> 3 I S I R R S
-#> 4 R R S S S S
-#> 5 R R S I R I
-#> 6 I R I I I R
+#> 1 S I R I S I
+#> 2 S R I S S R
+#> 3 S I S R I S
+#> 4 I S R R S S
+#> 5 S R R S S I
+#> 6 R S S I R S#> kanamycin#> 1 S#> 2 S
-#> 3 R
+#> 3 S#> 4 R#> 5 R
-#> 6 I
+#> 6 R
We can now add the interpretation of MDR-TB to our data set. You can
use:
Download as Apache
Feather file (0.1 MB)
@@ -904,40 +904,40 @@ inhibitors
clinical_breakpoints: Interpretation from MIC values
& disk diameters to SIR
-
A data set with 29 747 rows and 12 columns, containing the following
-column names: guideline, type, method, site,
-mo, rank_index, ab, ref_tbl,
-disk_dose, breakpoint_S, breakpoint_R, and
-uti.
+
A data set with 29 883 rows and 13 columns, containing the following
+column names: guideline, type, host, method,
+site, mo, rank_index, ab,
+ref_tbl, disk_dose, breakpoint_S,
+breakpoint_R, and uti.
This data set is in R available as clinical_breakpoints,
after you load the AMR package.
-
It was last updated on 20 October 2023 13:07:11 UTC. Find more info
+
It was last updated on 24 February 2024 14:16:52 UTC. Find more info
about the structure of this data set here.
(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support!)
-
Breaking
-
Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents a year ago
+
A New Milestone: One Health Support (= Human + Veterinary + Environmental)
+
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change. * as.sir() now supports animal breakpoints from CLSI. Use breakpoint_type = "animal" and set the host argument to a variable that contains animal species names. * The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page. * The antibiotics data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well. * ab_atc() now supports ATC codes of veterinary antibiotics (that all start with “Q”) * ab_url() now supports retrieving the WHOCC url of their ATCvet pages
+
+
+
Breaking
+
Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents over a year ago
-
New
-
Function group scale_*_mic(), namely: scale_x_mic(), scale_y_mic(), scale_colour_mic() and scale_fill_mic(). They are advanced ggplot2 extensions to allow plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
-
Function rescale_mic(), which allows to rescale MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
+
New functions
+
The group scale_*_mic(), namely: scale_x_mic(), scale_y_mic(), scale_colour_mic() and scale_fill_mic(). They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
+
+limit_mic_range(), which allows to limit MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
-
Changed
+
Changed
For MICs:
-
Added 4096 and 5 powers of 192 as valid levels (192, 384, 576, 768, 960)
-
Added new argument keep_operators to as.mic(). This can be "all" (default), "none", or "edges".
+
Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
+
Added new argument keep_operators to as.mic(). This can be "all" (default), "none", or "edges". This argument is also available in the new limit_mic_range() and scale_*_mic() functions.
Greatly improved vctrs integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that dplyr::rowwise() and dplyr::c_across() are now supported for e.g. columns of class mic. Despite this, this AMR package is still zero-dependent on any other package, including dplyr and vctrs.
AMR_custom_ab Allows to use custom antimicrobial drugs with this package. This is explained in add_custom_antimicrobials().
-
AMR_custom_mo Allows to use custom microorganisms with this package. This is explained in add_custom_microorganisms().
-
AMR_eucastrules Used for setting the default types of rules for eucast_rules() function, must be one or more of: "breakpoints", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expert").
-
AMR_guideline Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2023". Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
+
AMR_breakpoint_type A character to use in as.sir(), to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".
+
AMR_cleaning_regex A regular expression (case-insensitive) to use in as.mo() and all mo_* functions, to clean the user input. The default is the outcome of mo_cleaning_regex(), which removes texts between brackets and texts such as "species" and "serovar".
+
AMR_custom_ab A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in add_custom_antimicrobials().
+
AMR_custom_mo A file location to an RDS file, to use custom microorganisms with this package. This is explained in add_custom_microorganisms().
+
AMR_eucastrules A character to set the default types of rules for eucast_rules() function, must be one or more of: "breakpoints", "expert", "other", "custom", "all", and defaults to c("breakpoints", "expert").
+
AMR_guideline A character to set the default guideline for interpreting MIC values and disk diffusion diameters with as.sir(). Can be only the guideline name (e.g., "CLSI") or the name with a year (e.g. "CLSI 2019"). The default to the latest implemented EUCAST guideline, currently "EUCAST 2023". Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).
AMR_ignore_pattern A regular expression to ignore (i.e., make NA) any match given in as.mo() and all mo_* functions.
AMR_include_PKPD A logical to use in as.sir(), to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is TRUE.
-
AMR_ecoff A logical use in as.sir(), to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is FALSE.
AMR_include_screening A logical to use in as.sir(), to indicate that clinical breakpoints for screening are allowed - the default is FALSE.
AMR_keep_synonyms A logical to use in as.mo() and all mo_* functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is FALSE.
-
AMR_cleaning_regex A regular expression (case-insensitive) to use in as.mo() and all mo_* functions, to clean the user input. The default is the outcome of mo_cleaning_regex(), which removes texts between brackets and texts such as "species" and "serovar".
-
AMR_locale A language to use for the AMR package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported).
+
AMR_locale A character to set the language for the AMR package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).
AMR_mo_source A file location for a manual code list to be used in as.mo() and all mo_* functions. This is explained in set_mo_source().
@@ -187,14 +187,14 @@
Settings in R are not saved globally and are thus lost when R is exited. You can save your options to your own .Rprofile file, which is a user-specific file. You can edit it using:
to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with as.sir().
+
...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with as.sir().
Share Options Within Team
-
For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
+
For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
For each user, open the .Rprofile file using utils::file.edit("~/.Rprofile") and put in there:
Reload R/RStudio and check the settings with getOption(), e.g. getOption("AMR_locale") if you have set that value.
diff --git a/reference/AMR.html b/reference/AMR.html
index fbd451e8..beb8710b 100644
--- a/reference/AMR.html
+++ b/reference/AMR.html
@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
and doi:10.33612/diss.192486375
).
-After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
+After installing this package, R knows ~52 000 microorganisms (updated January 2024) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.">The AMR Package — AMR • AMR (for R)Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir • AMR (for R)
@@ -14,7 +24,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
@@ -164,9 +174,11 @@ All breakpoints used for interpretation are publicly available in the clinical_b
-
Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class sir, which is an ordered factor with levels S < I < R.
-
Currently available breakpoint guidelines are EUCAST 2011-2023 and CLSI 2011-2023, and available breakpoint types are "ECOFF", "animal", and "human".
-
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.
+
Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor with levels S < I < R.
+
Currently breakpoints are available:
For clinical microbiology from EUCAST 2011-2023 and CLSI 2011-2023;
+
For veterinary microbiology from EUCAST 2021-2023 and CLSI 2019-2023;
+
ECOFFs (Epidemiological cut-off values) from EUCAST 2020-2023 and CLSI 2022-2023.
+
All breakpoints used for interpretation are publicly available in the clinical_breakpoints data set.
@@ -192,6 +204,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
include_screening =getOption("AMR_include_screening", FALSE), include_PKPD =getOption("AMR_include_PKPD", TRUE), breakpoint_type =getOption("AMR_breakpoint_type", "human"),
+ host =NULL,...)
@@ -207,6 +220,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
include_screening =getOption("AMR_include_screening", FALSE), include_PKPD =getOption("AMR_include_PKPD", TRUE), breakpoint_type =getOption("AMR_breakpoint_type", "human"),
+ host =NULL,...)
@@ -222,21 +236,19 @@ All breakpoints used for interpretation are publicly available in the clinical_b
reference_data =AMR::clinical_breakpoints, include_screening =getOption("AMR_include_screening", FALSE), include_PKPD =getOption("AMR_include_PKPD", TRUE),
- breakpoint_type =getOption("AMR_breakpoint_type", "human")
+ breakpoint_type =getOption("AMR_breakpoint_type", "human"),
+ host =NULL)sir_interpretation_history(clean =FALSE)
-
-
Format
-
An object of class sir (inherits from ordered, factor) of length 1.
-
Source
-
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
Breakpoint tables for interpretation of MICs and zone diameters, 2011-2023, European Committee on Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.
+
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
EUCAST Breakpoint tables for interpretation of MICs and zone diameters, 2011-2023, European Committee on Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.
Arguments
@@ -289,7 +301,11 @@ All breakpoints used for interpretation are publicly available in the clinical_b
breakpoint_type
-
the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is "human", which can also be set with the package optionAMR_breakpoint_type.
+
the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is "human", which can also be set with the package optionAMR_breakpoint_type. If host is set to values of veterinary species, this will automatically be set to "animal".
+
+
+
host
+
a vector (or column name) with characters to indicate the host. Only useful for veterinary breakpoints, as it requires breakpoint_type = "animal". The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with set_AMR_locale() (though it will be automatically guessed based on the system language).
col_mo
@@ -310,19 +326,25 @@ All breakpoints used for interpretation are publicly available in the clinical_b
Details
-
Note: The clinical breakpoints in this package were validated through and imported from WHONET and the public use of this AMR package has been endorsed by CLSI and EUCAST, please see clinical_breakpoints for more information.
+
Note: The clinical breakpoints in this package were validated through, and imported from, WHONET. The public use of this AMR package has been endorsed by both CLSI and EUCAST. See clinical_breakpoints for more information.
How it Works
-
The as.sir() function works in four ways:
For cleaning raw / untransformed data. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as "<0.25; S" will be coerced to "S". Combined interpretations for multiple test methods (as seen in laboratory records) such as "S; S" will be coerced to "S", but a value like "S; I" will return NA with a warning that the input is unclear.
+
The as.sir() function can work in four ways:
For cleaning raw / untransformed data. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as "<0.25; S" will be coerced to "S". Combined interpretations for multiple test methods (as seen in laboratory records) such as "S; S" will be coerced to "S", but a value like "S; I" will return NA with a warning that the input is unclear.
For interpreting minimum inhibitory concentration (MIC) values according to EUCAST or CLSI. You must clean your MIC values first using as.mic(), that also gives your columns the new data class mic. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the mo argument.
Using dplyr, SIR interpretation can be done very easily with either:
+your_data %>%mutate(across(where(is.mic), as.sir))
+
+# for veterinary breakpoints, also set `host`:
+your_data %>%mutate_if(is.mic, as.sir, host ="column_with_animal_hosts", guideline ="CLSI")
Operators like "<=" will be stripped before interpretation. When using conserve_capped_values = TRUE, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (conserve_capped_values = FALSE) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
For interpreting disk diffusion diameters according to EUCAST or CLSI. You must clean your disk zones first using as.disk(), that also gives your columns the new data class disk. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the mo argument.
Using dplyr, SIR interpretation can be done very easily with either:
+your_data %>%mutate(across(where(is.disk), as.sir))
+
+# for veterinary breakpoints, also set `host`:
+your_data %>%mutate_if(is.disk, as.sir, host ="column_with_animal_hosts", guideline ="CLSI")
For interpreting a complete data set, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running as.sir(your_data).
For points 2, 3 and 4: Use sir_interpretation_history() to retrieve a data.frame (or tibble if the tibble package is installed) with all results of the last as.sir() call.
@@ -332,7 +354,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
Supported Guidelines
-
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023).
+
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for clinical microbiology: EUCAST 2011-2023 and CLSI 2011-2023, and for veterinary microbiology: EUCAST 2021-2023 and CLSI 2019-2023.
Thus, the guideline argument must be set to e.g., "EUCAST 2023" or "CLSI 2023". By simply using "EUCAST" (the default) or "CLSI" as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the reference_data argument. The guideline argument will then be ignored.
You can set the default guideline with the package optionAMR_guideline (e.g. in your .Rprofile file), such as:
options(AMR_guideline ="CLSI")
@@ -340,6 +362,9 @@ All breakpoints used for interpretation are publicly available in the clinical_b
options(AMR_guideline ="EUCAST 2020")# or to reset:options(AMR_guideline =NULL)
+
For veterinary guidelines, these might be the best options:
@@ -353,7 +378,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
Machine-Readable Clinical Breakpoints
-
The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 29 747 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+
The repository of this package contains a machine-readable version of all guidelines. This is a CSV file consisting of 29 883 rows and 13 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. This allows for easy implementation of these rules in laboratory information systems (LIS). Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
@@ -557,31 +582,31 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
#> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in#> Escherichia coli - assuming an unspecified body site. Use argument uti to#> set which isolates are from urine. See ?as.sir.
-#> => Assigning class 'sir' to already clean column 'ERY' (erythromycin)...
-#> OK.
+#> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...
+#> OK #> microorganism AMP CIP GEN TOB ERY#> 1 Escherichia coli S I S S R# return a 'logbook' about the results:sir_interpretation_history()
-#># A tibble: 13 × 13
+#># A tibble: 13 × 14#> datetime index ab_user mo_user ab mo input#><dttm><int><chr><chr><ab><mo><dbl>
-#> 1 2024-02-13 12:51:29 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16
-#> 2 2024-02-13 12:51:29 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18
-#> 3 2024-02-13 12:51:29 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256
-#> 4 2024-02-13 12:51:29 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8
-#> 5 2024-02-13 12:51:24 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01
-#> 6 2024-02-13 12:51:24 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2
-#> 7 2024-02-13 12:51:24 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4
-#> 8 2024-02-13 12:51:24 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8
-#> 9 2024-02-13 12:51:24 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2
-#>10 2024-02-13 12:51:23 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16
-#>11 2024-02-13 12:51:23 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18
-#>12 2024-02-13 12:51:23 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20
-#>13 2024-02-13 12:51:23 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18
-#># ℹ 6 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,
-#># guideline <chr>, ref_table <chr>, uti <lgl>
+#> 1 2024-02-24 17:56:35 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16
+#> 2 2024-02-24 17:56:35 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18
+#> 3 2024-02-24 17:56:35 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256
+#> 4 2024-02-24 17:56:34 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8
+#> 5 2024-02-24 17:56:30 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01
+#> 6 2024-02-24 17:56:30 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2
+#> 7 2024-02-24 17:56:30 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4
+#> 8 2024-02-24 17:56:30 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8
+#> 9 2024-02-24 17:56:30 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2
+#>10 2024-02-24 17:56:30 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16
+#>11 2024-02-24 17:56:29 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18
+#>12 2024-02-24 17:56:29 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20
+#>13 2024-02-24 17:56:29 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18
+#># ℹ 7 more variables: outcome <sir>, method <chr>, breakpoint_S_R <chr>,
+#># guideline <chr>, host <chr>, ref_table <chr>, uti <lgl># for single valuesas.sir(
diff --git a/reference/atc_online.html b/reference/atc_online.html
index 4102c648..a25085e7 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/reference/av_from_text.html b/reference/av_from_text.html
index 1f2ab597..03814a53 100644
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/reference/av_property.html b/reference/av_property.html
index e456f03a..57ae070a 100644
--- a/reference/av_property.html
+++ b/reference/av_property.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/reference/availability.html b/reference/availability.html
index 9776ff67..524edf91 100644
--- a/reference/availability.html
+++ b/reference/availability.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/reference/bug_drug_combinations.html b/reference/bug_drug_combinations.html
index 8b3fe00a..3babd459 100644
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
diff --git a/reference/clinical_breakpoints.html b/reference/clinical_breakpoints.html
index 8217ebc9..78348b27 100644
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@@ -1,5 +1,11 @@
-Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)
@@ -10,7 +16,7 @@
AMR (for R)
- 2.1.1.9004
+ 2.1.1.9008
@@ -160,7 +166,10 @@
-
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use as.sir() to transform MICs or disks measurements to SIR values.
+
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
+
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2023 and CLSI 2011-2023.
+
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2023 and CLSI 2019-2023.
+
Use as.sir() to transform MICs or disks measurements to SIR values.
@@ -170,8 +179,9 @@
Format
-
A tibble with 29 747 observations and 12 variables:
guideline Name of the guideline
+
A tibble with 29 883 observations and 13 variables:
guideline Name of the guideline
type Breakpoint type, either "ECOFF", "animal", or "human"
+
host Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"
method Testing method, either "DISK" or "MIC"
site Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
clinical_breakpoints
-#># A tibble: 29,747 × 12
-#> guideline type method site mo rank_index ab ref_tbl disk_dose
-#><chr><chr><chr><chr><mo><dbl><ab><chr><chr>
-#> 1 EUCAST 2… human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo… 10ug
-#> 2 EUCAST 2… human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo… NA
-#> 3 EUCAST 2… human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo… 1.25ug/2…
-#> 4 EUCAST 2… human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo… NA
-#> 5 EUCAST 2… human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo… 30ug/6ug
-#> 6 EUCAST 2… human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo… NA
-#> 7 EUCAST 2… human DISK NA B_ACNTB 3 AMK Acineto… 30ug
-#> 8 EUCAST 2… human DISK Unco… B_ACNTB 3 AMK Acineto… 30ug
-#> 9 EUCAST 2… human MIC NA B_ACNTB 3 AMK Acineto… NA
-#>10 EUCAST 2… human MIC Unco… B_ACNTB 3 AMK Acineto… NA
-#># ℹ 29,737 more rows
-#># ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl>
+#># A tibble: 29,883 × 13
+#> guideline type host method site mo rank_index ab ref_tbl
+#><chr><chr><chr><chr><chr><mo><dbl><ab><chr>
+#> 1 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 MEM A. xylo…
+#> 2 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 MEM A. xylo…
+#> 3 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 SXT A. xylo…
+#> 4 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 SXT A. xylo…
+#> 5 EUCAST 2023 human human DISK NA B_ACHRMB_XYLS 2 TZP A. xylo…
+#> 6 EUCAST 2023 human human MIC NA B_ACHRMB_XYLS 2 TZP A. xylo…
+#> 7 EUCAST 2023 human human DISK NA B_ACNTB 3 AMK Acineto…
+#> 8 EUCAST 2023 human human DISK Uncomp… B_ACNTB 3 AMK Acineto…
+#> 9 EUCAST 2023 human human MIC NA B_ACNTB 3 AMK Acineto…
+#>10 EUCAST 2023 human human MIC Uncomp… B_ACNTB 3 AMK Acineto…
+#># ℹ 29,873 more rows
+#># ℹ 4 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
+#># uti <lgl>