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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 1.5.0.9020
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Version: 1.5.0.9018
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Date: 2021-02-18
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Date: 2021-02-09
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
|
Authors@R: c(
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person(role = c("aut", "cre"),
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person(role = c("aut", "cre"),
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11
NEWS.md
11
NEWS.md
@ -1,5 +1,5 @@
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# AMR 1.5.0.9020
|
# AMR 1.5.0.9018
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## <small>Last updated: 18 February 2021</small>
|
## <small>Last updated: 9 February 2021</small>
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|
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### New
|
### New
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* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
|
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
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@ -7,10 +7,10 @@
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* Added data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
|
* Added data set `dosage` to fuel the new `eucast_dosage()` function and to make this data available in a structured way
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* Existing data set `example_isolates` now reflects the latest EUCAST rules
|
* Existing data set `example_isolates` now reflects the latest EUCAST rules
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* Added argument `only_rsi_columns` for some functions, which defaults to `FALSE`, to indicate if the functions must only be applied to columns that are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
|
* Added argument `only_rsi_columns` for some functions, which defaults to `FALSE`, to indicate if the functions must only be applied to columns that are of class `<rsi>` (i.e., transformed with `as.rsi()`). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:
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* All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglycosides()`, `carbapenems()`, `penicillins()`)
|
* All antibiotic selector functions (`ab_class()` and its wrappers, such as `aminoglocysides()`, `carbapenems()`, `penicillins()`)
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||||||
* All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglycosides()`, `filter_carbapenems()`, `filter_penicillins()`)
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* All antibiotic filter functions (`filter_ab_class()` and its wrappers, such as `filter_aminoglocysides()`, `filter_carbapenems()`, `filter_penicillins()`)
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* `eucast_rules()`
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* `eucast_rules()`
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* `mdro()` (including wrappers such as `brmo()`, `mrgn()` and `eucast_exceptional_phenotypes()`)
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* `mdro()` (including wrappers such as `brmo()`, `mrgn` and `eucast_exceptional_phenotypes()`)
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* `guess_ab_col()`
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* `guess_ab_col()`
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* Functions `oxazolidinones()` (an antibiotic selector function) and `filter_oxazolidinones()` (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
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* Functions `oxazolidinones()` (an antibiotic selector function) and `filter_oxazolidinones()` (an antibiotic filter function) to select/filter on e.g. linezolid and tedizolid
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||||||
```r
|
```r
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@ -57,7 +57,6 @@
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* Updated colours of values R, S and I in tibble printing
|
* Updated colours of values R, S and I in tibble printing
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||||||
* 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()`
|
* 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()`
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* 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.
|
* 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.
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* Fix for `mo_name()` when used in other languages than English
|
|
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|
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### Other
|
### Other
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* Big documentation updates
|
* Big documentation updates
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@ -82,27 +82,20 @@ check_dataset_integrity <- function() {
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# exception for example_isolates
|
# exception for example_isolates
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overwritten <- overwritten[overwritten != "example_isolates"]
|
overwritten <- overwritten[overwritten != "example_isolates"]
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if (length(overwritten) > 0) {
|
if (length(overwritten) > 0) {
|
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if (length(overwritten) > 1) {
|
warning_(ifelse(length(overwritten) == 1,
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plural <- c("s are", "", "s")
|
"The following data set is overwritten by your global environment and prevents the AMR package from working correctly: ",
|
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} else {
|
"The following data sets are overwritten by your global environment and prevent the AMR package from working correctly: "),
|
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plural <- c(" is", "s", "")
|
|
||||||
}
|
|
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warning_("The following data set", plural[1],
|
|
||||||
" overwritten by your global environment and prevent", plural[2],
|
|
||||||
" the AMR package from working correctly: ",
|
|
||||||
vector_and(overwritten, quotes = "'"),
|
vector_and(overwritten, quotes = "'"),
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".\nPlease rename your object", plural[3], ".", call = FALSE)
|
".\nPlease rename your object(s).", call = FALSE)
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}
|
}
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# check if other packages did not overwrite our data sets
|
# check if other packages did not overwrite our data sets
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valid_microorganisms <- TRUE
|
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valid_antibiotics <- TRUE
|
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tryCatch({
|
tryCatch({
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valid_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
|
check_microorganisms <- all(c("mo", "fullname", "kingdom", "phylum",
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"class", "order", "family", "genus",
|
"class", "order", "family", "genus",
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"species", "subspecies", "rank",
|
"species", "subspecies", "rank",
|
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"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
|
"species_id", "source", "ref", "prevalence") %in% colnames(microorganisms),
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na.rm = TRUE)
|
na.rm = TRUE)
|
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valid_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
|
check_antibiotics <- all(c("ab", "atc", "cid", "name", "group",
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"atc_group1", "atc_group2", "abbreviations",
|
"atc_group1", "atc_group2", "abbreviations",
|
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"synonyms", "oral_ddd", "oral_units",
|
"synonyms", "oral_ddd", "oral_units",
|
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"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
|
"iv_ddd", "iv_units", "loinc") %in% colnames(antibiotics),
|
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@ -111,7 +104,7 @@ check_dataset_integrity <- function() {
|
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# package not yet loaded
|
# package not yet loaded
|
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require("AMR")
|
require("AMR")
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})
|
})
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stop_if(!valid_microorganisms | !valid_antibiotics,
|
stop_if(!check_microorganisms | !check_antibiotics,
|
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"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
|
"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
|
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invisible(TRUE)
|
invisible(TRUE)
|
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}
|
}
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|
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@ -43,7 +43,7 @@
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#' # See ?example_isolates.
|
#' # See ?example_isolates.
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#'
|
#'
|
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#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
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#' example_isolates[, carbapenems()]
|
#' example_isolates[, c(carbapenems())]
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#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
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#' example_isolates[, c("mo", aminoglycosides())]
|
#' example_isolates[, c("mo", aminoglycosides())]
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#'
|
#'
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|
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@ -172,10 +172,7 @@ mo_name <- function(x, language = get_locale(), ...) {
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meet_criteria(x, allow_NA = TRUE)
|
meet_criteria(x, allow_NA = TRUE)
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meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
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|
|
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translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
|
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
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language = language,
|
|
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only_unknown = FALSE,
|
|
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affect_mo_name = TRUE)
|
|
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}
|
}
|
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|
|
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#' @rdname mo_property
|
#' @rdname mo_property
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@ -217,7 +214,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
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|
|
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shortnames[is.na(x.mo)] <- NA_character_
|
shortnames[is.na(x.mo)] <- NA_character_
|
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load_mo_failures_uncertainties_renamed(metadata)
|
load_mo_failures_uncertainties_renamed(metadata)
|
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translate_AMR(shortnames, language = language, only_unknown = FALSE, affect_mo_name = TRUE)
|
translate_AMR(shortnames, language = language, only_unknown = FALSE)
|
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}
|
}
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|
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#' @rdname mo_property
|
#' @rdname mo_property
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|
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -123,7 +123,7 @@ coerce_language_setting <- function(lang) {
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}
|
}
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|
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# translate strings based on inst/translations.tsv
|
# translate strings based on inst/translations.tsv
|
||||||
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, affect_mo_name = FALSE) {
|
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
|
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|
|
||||||
if (is.null(language)) {
|
if (is.null(language)) {
|
||||||
return(from)
|
return(from)
|
||||||
@ -146,13 +146,10 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
|
|||||||
if (only_unknown == TRUE) {
|
if (only_unknown == TRUE) {
|
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df_trans <- subset(df_trans, pattern %like% "unknown")
|
df_trans <- subset(df_trans, pattern %like% "unknown")
|
||||||
}
|
}
|
||||||
if (affect_mo_name == TRUE) {
|
|
||||||
df_trans <- subset(df_trans, affect_mo_name == TRUE)
|
|
||||||
}
|
|
||||||
|
|
||||||
# default: case sensitive if value if 'ignore.case' is missing:
|
# default case sensitive if value if 'ignore.case' is missing:
|
||||||
df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
|
df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
|
||||||
# default: not using regular expressions (fixed = TRUE) if 'fixed' is missing:
|
# default not using regular expressions (fixed = TRUE) if 'fixed' is missing:
|
||||||
df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
|
df_trans$fixed[is.na(df_trans$fixed)] <- TRUE
|
||||||
|
|
||||||
# check if text to look for is in one of the patterns
|
# check if text to look for is in one of the patterns
|
||||||
@ -170,8 +167,7 @@ translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE, a
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replacement = df_trans$replacement[i],
|
replacement = df_trans$replacement[i],
|
||||||
x = from_unique_translated,
|
x = from_unique_translated,
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ignore.case = df_trans$ignore.case[i],
|
ignore.case = df_trans$ignore.case[i],
|
||||||
fixed = df_trans$fixed[i],
|
fixed = df_trans$fixed[i]))
|
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perl = !df_trans$fixed[i]))
|
|
||||||
|
|
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# force UTF-8 for diacritics
|
# force UTF-8 for diacritics
|
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from_unique_translated <- enc2utf8(from_unique_translated)
|
from_unique_translated <- enc2utf8(from_unique_translated)
|
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@ -10,7 +10,7 @@
|
|||||||
|
|
||||||
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
|
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
|
||||||
|
|
||||||
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](data-raw).
|
The latest built **source package** (`AMR_x.x.x.tar.gz`) can be found in folder [/data-raw/](data-raw).
|
||||||
|
|
||||||
`AMR` is a free, open-source and independent R package 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.
|
`AMR` is a free, open-source and independent R package 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.
|
||||||
|
|
||||||
@ -20,7 +20,7 @@ This package is fully independent of any other R package and works on Windows, m
|
|||||||
|
|
||||||
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package.
|
This is the development source of the `AMR` package for R. Not a developer? Then please visit our website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package.
|
||||||
|
|
||||||
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to our university's Gitea server (https://git.web.rug.nl/P281424/AMR) and to GitLab (https://gitlab.com/msberends/AMR).*
|
*NOTE: this source code is on GitHub (https://github.com/msberends/AMR), but also automatically mirrored to GitLab (https://gitlab.com/msberends/AMR).*
|
||||||
|
|
||||||
### How to get this package
|
### How to get this package
|
||||||
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
|
Please see [our website](https://msberends.github.io/AMR/#get-this-package).
|
||||||
|
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Binary file not shown.
@ -25,22 +25,20 @@
|
|||||||
|
|
||||||
# Reproduction of the `microorganisms` data set
|
# Reproduction of the `microorganisms` data set
|
||||||
|
|
||||||
# Data retrieved from the Catalogue of Life (CoL):
|
# Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
|
||||||
# https://download.catalogueoflife.org/col/monthly/life/
|
# https://opendata.eol.org/dataset/catalogue-of-life/
|
||||||
# (download latest dwca, such as https://download.catalogueoflife.org/col/monthly/2020-12-01_dwca.zip)
|
|
||||||
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
|
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
|
||||||
# https://doi.org/10.15468/rffz4x
|
# https://doi.org/10.15468/rffz4x
|
||||||
#
|
#
|
||||||
# And from the List of Prokaryotic names with Standing in Nomenclature (LPSN)
|
# And from the Leibniz Institute: German Collection of Microorganisms and Cell Cultures (DSMZ)
|
||||||
# (register first) https://lpsn.dsmz.de/downloads
|
# (register first at https://bacdive.dsmz.de/api/pnu/registration/register/ and use API as done below)
|
||||||
# download the latest CSV file.
|
|
||||||
|
|
||||||
library(dplyr)
|
library(dplyr)
|
||||||
library(AMR)
|
library(AMR)
|
||||||
# also needed: data.table, httr, jsonlite, cleaner, stringr
|
# also needed: data.table, httr, jsonlite, cleaner, stringr
|
||||||
|
|
||||||
# unzip and extract taxa.txt (both around 1.5 GB, 3.7-3.9M rows) from Col and GBIF, then:
|
# unzip and extract taxa.txt (both around 1.5 GB, 3.7-3.9M rows) from Col and GBIF, then:
|
||||||
data_col_raw <- data.table::fread("data-raw/taxon.tsv", quote = "")
|
data_col_raw <- data.table::fread("data-raw/taxon.tab", quote = "")
|
||||||
data_gbif <- data.table::fread("data-raw/taxa.txt", quote = "")
|
data_gbif <- data.table::fread("data-raw/taxa.txt", quote = "")
|
||||||
|
|
||||||
# merge the two
|
# merge the two
|
||||||
|
|||||||
@ -1,412 +1,407 @@
|
|||||||
lang pattern replacement fixed ignore.case affect_mo_name
|
lang pattern replacement fixed ignore.case
|
||||||
de Coagulase-negative Staphylococcus Koagulase-negative Staphylococcus FALSE FALSE TRUE
|
de Coagulase-negative Staphylococcus Koagulase-negative Staphylococcus FALSE FALSE
|
||||||
de Coagulase-positive Staphylococcus Koagulase-positive Staphylococcus FALSE FALSE TRUE
|
de Coagulase-positive Staphylococcus Koagulase-positive Staphylococcus FALSE FALSE
|
||||||
de Beta-haemolytic Streptococcus Beta-hämolytischer Streptococcus FALSE FALSE TRUE
|
de Beta-haemolytic Streptococcus Beta-hämolytischer Streptococcus FALSE FALSE
|
||||||
de unknown Gram-negatives unbekannte Gramnegativen FALSE FALSE TRUE
|
de unknown Gram-negatives unbekannte Gramnegativen FALSE FALSE
|
||||||
de unknown Gram-positives unbekannte Grampositiven FALSE FALSE TRUE
|
de unknown Gram-positives unbekannte Grampositiven FALSE FALSE
|
||||||
de unknown fungus unbekannter Pilze FALSE FALSE TRUE
|
de unknown name unbekannte Name FALSE FALSE
|
||||||
de unknown yeast unbekannte Hefe FALSE FALSE TRUE
|
de unknown kingdom unbekanntes Reich FALSE FALSE
|
||||||
de unknown name unbekannte Name FALSE FALSE TRUE
|
de unknown phylum unbekannter Stamm FALSE FALSE
|
||||||
de unknown kingdom unbekanntes Reich FALSE FALSE TRUE
|
de unknown class unbekannte Klasse FALSE FALSE
|
||||||
de unknown phylum unbekannter Stamm FALSE FALSE TRUE
|
de unknown order unbekannte Ordnung FALSE FALSE
|
||||||
de unknown class unbekannte Klasse FALSE FALSE TRUE
|
de unknown family unbekannte Familie FALSE FALSE
|
||||||
de unknown order unbekannte Ordnung FALSE FALSE TRUE
|
de unknown genus unbekannte Gattung FALSE FALSE
|
||||||
de unknown family unbekannte Familie FALSE FALSE TRUE
|
de unknown species unbekannte Art FALSE FALSE
|
||||||
de unknown genus unbekannte Gattung FALSE FALSE TRUE
|
de unknown subspecies unbekannte Unterart FALSE FALSE
|
||||||
de unknown species unbekannte Art FALSE FALSE TRUE
|
de unknown rank unbekannter Rang FALSE FALSE
|
||||||
de unknown subspecies unbekannte Unterart FALSE FALSE TRUE
|
de CoNS KNS TRUE FALSE
|
||||||
de unknown rank unbekannter Rang FALSE FALSE TRUE
|
de CoPS KPS TRUE FALSE
|
||||||
de CoNS KNS TRUE FALSE TRUE
|
de Gram-negative Gramnegativ FALSE FALSE
|
||||||
de CoPS KPS TRUE FALSE TRUE
|
de Gram-positive Grampositiv FALSE FALSE
|
||||||
de Gram-negative Gramnegativ FALSE FALSE FALSE
|
de Bacteria Bakterien FALSE FALSE
|
||||||
de Gram-positive Grampositiv FALSE FALSE FALSE
|
de Fungi Pilze FALSE FALSE
|
||||||
de ^Bacteria$ Bakterien FALSE FALSE FALSE
|
de Yeasts Hefen FALSE FALSE
|
||||||
de ^Fungi$ Pilze FALSE FALSE FALSE
|
de Protozoa Protozoen FALSE FALSE
|
||||||
de ^Yeasts$ Hefen FALSE FALSE FALSE
|
de biogroup Biogruppe FALSE FALSE
|
||||||
de ^Protozoa$ Protozoen FALSE FALSE FALSE
|
de biotype Biotyp FALSE FALSE
|
||||||
de biogroup Biogruppe FALSE FALSE FALSE
|
de vegetative vegetativ FALSE FALSE
|
||||||
de biotype Biotyp FALSE FALSE FALSE
|
de ([([ ]*?)group \\1Gruppe FALSE FALSE
|
||||||
de vegetative vegetativ FALSE FALSE FALSE
|
de ([([ ]*?)Group \\1Gruppe FALSE FALSE
|
||||||
de ([([ ]*?)group \\1Gruppe FALSE FALSE FALSE
|
de no .*growth keine? .*wachstum FALSE TRUE
|
||||||
de ([([ ]*?)Group \\1Gruppe FALSE FALSE FALSE
|
de no|not keine? FALSE TRUE
|
||||||
de no .*growth keine? .*wachstum FALSE TRUE FALSE
|
|
||||||
de (^| )no|not keine? FALSE TRUE FALSE
|
nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
|
||||||
nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE TRUE
|
nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
|
||||||
nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE TRUE
|
nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE
|
||||||
nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE TRUE
|
nl unknown Gram-negatives onbekende Gram-negatieven FALSE FALSE
|
||||||
nl unknown Gram-negatives onbekende Gram-negatieven FALSE FALSE TRUE
|
nl unknown Gram-positives onbekende Gram-positieven FALSE FALSE
|
||||||
nl unknown Gram-positives onbekende Gram-positieven FALSE FALSE TRUE
|
nl unknown name onbekende naam FALSE FALSE
|
||||||
nl unknown fungus onbekende schimmel FALSE FALSE TRUE
|
nl unknown kingdom onbekend koninkrijk FALSE FALSE
|
||||||
nl unknown yeast onbekende gist FALSE FALSE TRUE
|
nl unknown phylum onbekend fylum FALSE FALSE
|
||||||
nl unknown name onbekende naam FALSE FALSE TRUE
|
nl unknown class onbekende klasse FALSE FALSE
|
||||||
nl unknown kingdom onbekend koninkrijk FALSE FALSE TRUE
|
nl unknown order onbekende orde FALSE FALSE
|
||||||
nl unknown phylum onbekend fylum FALSE FALSE TRUE
|
nl unknown family onbekende familie FALSE FALSE
|
||||||
nl unknown class onbekende klasse FALSE FALSE TRUE
|
nl unknown genus onbekend geslacht FALSE FALSE
|
||||||
nl unknown order onbekende orde FALSE FALSE TRUE
|
nl unknown species onbekende soort FALSE FALSE
|
||||||
nl unknown family onbekende familie FALSE FALSE TRUE
|
nl unknown subspecies onbekende ondersoort FALSE FALSE
|
||||||
nl unknown genus onbekend geslacht FALSE FALSE TRUE
|
nl unknown rank onbekende rang FALSE FALSE
|
||||||
nl unknown species onbekende soort FALSE FALSE TRUE
|
nl CoNS CNS TRUE FALSE
|
||||||
nl unknown subspecies onbekende ondersoort FALSE FALSE TRUE
|
nl CoPS CPS TRUE FALSE
|
||||||
nl unknown rank onbekende rang FALSE FALSE TRUE
|
nl Gram-negative Gram-negatief FALSE FALSE
|
||||||
nl CoNS CNS TRUE FALSE TRUE
|
nl Gram-positive Gram-positief FALSE FALSE
|
||||||
nl CoPS CPS TRUE FALSE TRUE
|
nl Bacteria Bacteriën FALSE FALSE
|
||||||
nl Gram-negative Gram-negatief FALSE FALSE FALSE
|
nl Fungi Schimmels FALSE FALSE
|
||||||
nl Gram-positive Gram-positief FALSE FALSE FALSE
|
nl Yeasts Gisten FALSE FALSE
|
||||||
nl ^Bacteria$ Bacteriën FALSE FALSE FALSE
|
nl Protozoa Protozoën FALSE FALSE
|
||||||
nl ^Fungi$ Schimmels FALSE FALSE FALSE
|
nl biogroup biogroep FALSE FALSE
|
||||||
nl ^Yeasts$ Gisten FALSE FALSE FALSE
|
nl vegetative vegetatief FALSE FALSE
|
||||||
nl ^Protozoa$ Protozoën FALSE FALSE FALSE
|
nl ([([ ]*?)group \\1groep FALSE FALSE
|
||||||
nl biogroup biogroep FALSE FALSE FALSE
|
nl ([([ ]*?)Group \\1Groep FALSE FALSE
|
||||||
nl vegetative vegetatief FALSE FALSE FALSE
|
nl antibiotic antibioticum FALSE FALSE
|
||||||
nl ([([ ]*?)group \\1groep FALSE FALSE FALSE
|
nl Antibiotic Antibioticum FALSE FALSE
|
||||||
nl ([([ ]*?)Group \\1Groep FALSE FALSE FALSE
|
nl Drug Middel FALSE FALSE
|
||||||
nl antibiotic antibioticum FALSE FALSE FALSE
|
nl drug middel FALSE FALSE
|
||||||
nl Antibiotic Antibioticum FALSE FALSE FALSE
|
nl no .*growth geen .*groei FALSE TRUE
|
||||||
nl Drug Middel FALSE FALSE FALSE
|
nl no|not geen|niet FALSE TRUE
|
||||||
nl drug middel FALSE FALSE FALSE
|
|
||||||
nl no .*growth geen .*groei FALSE TRUE FALSE
|
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
|
||||||
nl no|not geen|niet FALSE TRUE FALSE
|
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
|
||||||
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE TRUE
|
es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||||
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE TRUE
|
es unknown Gram-negatives Gram negativos desconocidos FALSE FALSE
|
||||||
es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE TRUE
|
es unknown Gram-positives Gram positivos desconocidos FALSE FALSE
|
||||||
es unknown Gram-negatives Gram negativos desconocidos FALSE FALSE TRUE
|
es unknown name nombre desconocido FALSE FALSE
|
||||||
es unknown Gram-positives Gram positivos desconocidos FALSE FALSE TRUE
|
es unknown kingdom reino desconocido FALSE FALSE
|
||||||
es unknown fungus hongo desconocido FALSE FALSE TRUE
|
es unknown phylum filo desconocido FALSE FALSE
|
||||||
es unknown yeast levadura desconocida FALSE FALSE TRUE
|
es unknown class clase desconocida FALSE FALSE
|
||||||
es unknown name nombre desconocido FALSE FALSE TRUE
|
es unknown order orden desconocido FALSE FALSE
|
||||||
es unknown kingdom reino desconocido FALSE FALSE TRUE
|
es unknown family familia desconocida FALSE FALSE
|
||||||
es unknown phylum filo desconocido FALSE FALSE TRUE
|
es unknown genus género desconocido FALSE FALSE
|
||||||
es unknown class clase desconocida FALSE FALSE TRUE
|
es unknown species especie desconocida FALSE FALSE
|
||||||
es unknown order orden desconocido FALSE FALSE TRUE
|
es unknown subspecies subespecie desconocida FALSE FALSE
|
||||||
es unknown family familia desconocida FALSE FALSE TRUE
|
es unknown rank rango desconocido FALSE FALSE
|
||||||
es unknown genus género desconocido FALSE FALSE TRUE
|
es CoNS SCN TRUE FALSE
|
||||||
es unknown species especie desconocida FALSE FALSE TRUE
|
es CoPS SCP TRUE FALSE
|
||||||
es unknown subspecies subespecie desconocida FALSE FALSE TRUE
|
es Gram-negative Gram negativo FALSE FALSE
|
||||||
es unknown rank rango desconocido FALSE FALSE TRUE
|
es Gram-positive Gram positivo FALSE FALSE
|
||||||
es CoNS SCN TRUE FALSE TRUE
|
es Bacteria Bacterias FALSE FALSE
|
||||||
es CoPS SCP TRUE FALSE TRUE
|
es Fungi Hongos FALSE FALSE
|
||||||
es Gram-negative Gram negativo FALSE FALSE FALSE
|
es Yeasts Levaduras FALSE FALSE
|
||||||
es Gram-positive Gram positivo FALSE FALSE FALSE
|
es Protozoa Protozoarios FALSE FALSE
|
||||||
es ^Bacteria$ Bacterias FALSE FALSE FALSE
|
es biogroup biogrupo FALSE FALSE
|
||||||
es ^Fungi$ Hongos FALSE FALSE FALSE
|
es biotype biotipo FALSE FALSE
|
||||||
es ^Yeasts$ Levaduras FALSE FALSE FALSE
|
es vegetative vegetativo FALSE FALSE
|
||||||
es ^Protozoa$ Protozoarios FALSE FALSE FALSE
|
es ([([ ]*?)group \\1grupo FALSE FALSE
|
||||||
es biogroup biogrupo FALSE FALSE FALSE
|
es ([([ ]*?)Group \\1Grupo FALSE FALSE
|
||||||
es biotype biotipo FALSE FALSE FALSE
|
es no .*growth no .*crecimientonon FALSE TRUE
|
||||||
es vegetative vegetativo FALSE FALSE FALSE
|
es no|not no|sin FALSE TRUE
|
||||||
es ([([ ]*?)group \\1grupo FALSE FALSE FALSE
|
|
||||||
es ([([ ]*?)Group \\1Grupo FALSE FALSE FALSE
|
it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
|
||||||
es no .*growth no .*crecimientonon FALSE TRUE FALSE
|
it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
|
||||||
es no|not no|sin FALSE TRUE FALSE
|
it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE
|
||||||
it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE TRUE
|
it unknown Gram-negatives Gram negativi sconosciuti FALSE FALSE
|
||||||
it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE TRUE
|
it unknown Gram-positives Gram positivi sconosciuti FALSE FALSE
|
||||||
it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE TRUE
|
it unknown name nome sconosciuto FALSE FALSE
|
||||||
it unknown Gram-negatives Gram negativi sconosciuti FALSE FALSE TRUE
|
it unknown kingdom regno sconosciuto FALSE FALSE
|
||||||
it unknown Gram-positives Gram positivi sconosciuti FALSE FALSE TRUE
|
it unknown phylum phylum sconosciuto FALSE FALSE
|
||||||
it unknown fungus fungo sconosciuto FALSE FALSE TRUE
|
it unknown class classe sconosciuta FALSE FALSE
|
||||||
it unknown yeast lievito sconosciuto FALSE FALSE TRUE
|
it unknown order ordine sconosciuto FALSE FALSE
|
||||||
it unknown name nome sconosciuto FALSE FALSE TRUE
|
it unknown family famiglia sconosciuta FALSE FALSE
|
||||||
it unknown kingdom regno sconosciuto FALSE FALSE TRUE
|
it unknown genus genere sconosciuto FALSE FALSE
|
||||||
it unknown phylum phylum sconosciuto FALSE FALSE TRUE
|
it unknown species specie sconosciute FALSE FALSE
|
||||||
it unknown class classe sconosciuta FALSE FALSE TRUE
|
it unknown subspecies sottospecie sconosciute FALSE FALSE
|
||||||
it unknown order ordine sconosciuto FALSE FALSE TRUE
|
it unknown rank grado sconosciuto FALSE FALSE
|
||||||
it unknown family famiglia sconosciuta FALSE FALSE TRUE
|
it Gram-negative Gram negativo FALSE FALSE
|
||||||
it unknown genus genere sconosciuto FALSE FALSE TRUE
|
it Gram-positive Gram positivo FALSE FALSE
|
||||||
it unknown species specie sconosciute FALSE FALSE TRUE
|
it Bacteria Batteri FALSE FALSE
|
||||||
it unknown subspecies sottospecie sconosciute FALSE FALSE TRUE
|
it Fungi Funghi FALSE FALSE
|
||||||
it unknown rank grado sconosciuto FALSE FALSE TRUE
|
it Yeasts Lieviti FALSE FALSE
|
||||||
it Gram-negative Gram negativo FALSE FALSE FALSE
|
it Protozoa Protozoi FALSE FALSE
|
||||||
it Gram-positive Gram positivo FALSE FALSE FALSE
|
it biogroup biogruppo FALSE FALSE
|
||||||
it ^Bacteria$ Batteri FALSE FALSE FALSE
|
it biotype biotipo FALSE FALSE
|
||||||
it ^Fungi$ Funghi FALSE FALSE FALSE
|
it vegetative vegetativo FALSE FALSE
|
||||||
it ^Yeasts$ Lieviti FALSE FALSE FALSE
|
it ([([ ]*?)group \\1gruppo FALSE FALSE
|
||||||
it ^Protozoa$ Protozoi FALSE FALSE FALSE
|
it ([([ ]*?)Group \\1Gruppo FALSE FALSE
|
||||||
it biogroup biogruppo FALSE FALSE FALSE
|
it no .*growth sem .*crescimento FALSE TRUE
|
||||||
it biotype biotipo FALSE FALSE FALSE
|
it no|not sem FALSE TRUE
|
||||||
it vegetative vegetativo FALSE FALSE FALSE
|
|
||||||
it ([([ ]*?)group \\1gruppo FALSE FALSE FALSE
|
fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE
|
||||||
it ([([ ]*?)Group \\1Gruppo FALSE FALSE FALSE
|
fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
|
||||||
it no .*growth sem .*crescimento FALSE TRUE FALSE
|
fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE
|
||||||
it no|not sem FALSE TRUE FALSE
|
fr unknown Gram-negatives Gram négatifs inconnus FALSE FALSE
|
||||||
fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE TRUE
|
fr unknown Gram-positives Gram positifs inconnus FALSE FALSE
|
||||||
fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE TRUE
|
fr unknown name nom inconnu FALSE FALSE
|
||||||
fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE TRUE
|
fr unknown kingdom règme inconnu FALSE FALSE
|
||||||
fr unknown Gram-negatives Gram négatifs inconnus FALSE FALSE TRUE
|
fr unknown phylum embranchement inconnu FALSE FALSE
|
||||||
fr unknown Gram-positives Gram positifs inconnus FALSE FALSE TRUE
|
fr unknown class classe inconnue FALSE FALSE
|
||||||
fr unknown fungus champignon inconnu FALSE FALSE TRUE
|
fr unknown order ordre inconnu FALSE FALSE
|
||||||
fr unknown yeast levure inconnue FALSE FALSE TRUE
|
fr unknown family famille inconnue FALSE FALSE
|
||||||
fr unknown name nom inconnu FALSE FALSE TRUE
|
fr unknown genus genre inconnu FALSE FALSE
|
||||||
fr unknown kingdom règme inconnu FALSE FALSE TRUE
|
fr unknown species espèce inconnue FALSE FALSE
|
||||||
fr unknown phylum embranchement inconnu FALSE FALSE TRUE
|
fr unknown subspecies sous-espèce inconnue FALSE FALSE
|
||||||
fr unknown class classe inconnue FALSE FALSE TRUE
|
fr unknown rank rang inconnu FALSE FALSE
|
||||||
fr unknown order ordre inconnu FALSE FALSE TRUE
|
fr Gram-negative Gram négatif FALSE FALSE
|
||||||
fr unknown family famille inconnue FALSE FALSE TRUE
|
fr Gram-positive Gram positif FALSE FALSE
|
||||||
fr unknown genus genre inconnu FALSE FALSE TRUE
|
fr Bacteria Bactéries FALSE FALSE
|
||||||
fr unknown species espèce inconnue FALSE FALSE TRUE
|
fr Fungi Champignons FALSE FALSE
|
||||||
fr unknown subspecies sous-espèce inconnue FALSE FALSE TRUE
|
fr Yeasts Levures FALSE FALSE
|
||||||
fr unknown rank rang inconnu FALSE FALSE TRUE
|
fr Protozoa Protozoaires FALSE FALSE
|
||||||
fr Gram-negative Gram négatif FALSE FALSE FALSE
|
fr biogroup biogroupe FALSE FALSE
|
||||||
fr Gram-positive Gram positif FALSE FALSE FALSE
|
fr vegetative végétatif FALSE FALSE
|
||||||
fr ^Bacteria$ Bactéries FALSE FALSE FALSE
|
fr ([([ ]*?)group \\1groupe FALSE FALSE
|
||||||
fr ^Fungi$ Champignons FALSE FALSE FALSE
|
fr ([([ ]*?)Group \\1Groupe FALSE FALSE
|
||||||
fr ^Yeasts$ Levures FALSE FALSE FALSE
|
fr no .*growth pas .*croissance FALSE TRUE
|
||||||
fr ^Protozoa$ Protozoaires FALSE FALSE FALSE
|
fr no|not non FALSE TRUE
|
||||||
fr biogroup biogroupe FALSE FALSE FALSE
|
|
||||||
fr vegetative végétatif FALSE FALSE FALSE
|
pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE
|
||||||
fr ([([ ]*?)group \\1groupe FALSE FALSE FALSE
|
pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE
|
||||||
fr ([([ ]*?)Group \\1Groupe FALSE FALSE FALSE
|
pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||||
fr no .*growth pas .*croissance FALSE TRUE FALSE
|
pt unknown Gram-negatives Gram negativos desconhecidos FALSE FALSE
|
||||||
fr no|not non FALSE TRUE FALSE
|
pt unknown Gram-positives Gram positivos desconhecidos FALSE FALSE
|
||||||
pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE TRUE
|
pt unknown name nome desconhecido FALSE FALSE
|
||||||
pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE TRUE
|
pt unknown kingdom reino desconhecido FALSE FALSE
|
||||||
pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE TRUE
|
pt unknown phylum filo desconhecido FALSE FALSE
|
||||||
pt unknown Gram-negatives Gram negativos desconhecidos FALSE FALSE TRUE
|
pt unknown class classe desconhecida FALSE FALSE
|
||||||
pt unknown Gram-positives Gram positivos desconhecidos FALSE FALSE TRUE
|
pt unknown order ordem desconhecido FALSE FALSE
|
||||||
pt unknown fungus fungo desconhecido FALSE FALSE TRUE
|
pt unknown family família desconhecida FALSE FALSE
|
||||||
pt unknown yeast levedura desconhecida FALSE FALSE TRUE
|
pt unknown genus gênero desconhecido FALSE FALSE
|
||||||
pt unknown name nome desconhecido FALSE FALSE TRUE
|
pt unknown species espécies desconhecida FALSE FALSE
|
||||||
pt unknown kingdom reino desconhecido FALSE FALSE TRUE
|
pt unknown subspecies subespécies desconhecida FALSE FALSE
|
||||||
pt unknown phylum filo desconhecido FALSE FALSE TRUE
|
pt unknown rank classificação desconhecido FALSE FALSE
|
||||||
pt unknown class classe desconhecida FALSE FALSE TRUE
|
pt Gram-negative Gram negativo FALSE FALSE
|
||||||
pt unknown order ordem desconhecido FALSE FALSE TRUE
|
pt Gram-positive Gram positivo FALSE FALSE
|
||||||
pt unknown family família desconhecida FALSE FALSE TRUE
|
pt Bacteria Bactérias FALSE FALSE
|
||||||
pt unknown genus gênero desconhecido FALSE FALSE TRUE
|
pt Fungi Fungos FALSE FALSE
|
||||||
pt unknown species espécies desconhecida FALSE FALSE TRUE
|
pt Yeasts Leveduras FALSE FALSE
|
||||||
pt unknown subspecies subespécies desconhecida FALSE FALSE TRUE
|
pt Protozoa Protozoários FALSE FALSE
|
||||||
pt unknown rank classificação desconhecido FALSE FALSE TRUE
|
pt biogroup biogrupo FALSE FALSE
|
||||||
pt Gram-negative Gram negativo FALSE FALSE FALSE
|
pt biotype biótipo FALSE FALSE
|
||||||
pt Gram-positive Gram positivo FALSE FALSE FALSE
|
pt vegetative vegetativo FALSE FALSE
|
||||||
pt ^Bacteria$ Bactérias FALSE FALSE FALSE
|
pt ([([ ]*?)group \\1grupo FALSE FALSE
|
||||||
pt ^Fungi$ Fungos FALSE FALSE FALSE
|
pt ([([ ]*?)Group \\1Grupo FALSE FALSE
|
||||||
pt ^Yeasts$ Leveduras FALSE FALSE FALSE
|
pt no .*growth sem .*crescimento FALSE TRUE
|
||||||
pt ^Protozoa$ Protozoários FALSE FALSE FALSE
|
pt no|not sem FALSE TRUE
|
||||||
pt biogroup biogrupo FALSE FALSE FALSE
|
|
||||||
pt biotype biótipo FALSE FALSE FALSE
|
de clavulanic acid Clavulansäure FALSE TRUE
|
||||||
pt vegetative vegetativo FALSE FALSE FALSE
|
|
||||||
pt ([([ ]*?)group \\1grupo FALSE FALSE FALSE
|
nl 4-aminosalicylic acid 4-aminosalicylzuur
|
||||||
pt ([([ ]*?)Group \\1Grupo FALSE FALSE FALSE
|
nl Adefovir dipivoxil Adefovir
|
||||||
pt no .*growth sem .*crescimento FALSE TRUE FALSE
|
nl Aldesulfone sodium Aldesulfon
|
||||||
pt no|not sem FALSE TRUE FALSE
|
nl Amikacin Amikacine
|
||||||
de clavulanic acid Clavulansäure FALSE TRUE FALSE
|
nl Amoxicillin Amoxicilline
|
||||||
nl 4-aminosalicylic acid 4-aminosalicylzuur TRUE FALSE FALSE
|
nl Amoxicillin/beta-lactamase inhibitor Amoxicilline/enzymremmer
|
||||||
nl Adefovir dipivoxil Adefovir TRUE FALSE FALSE
|
nl Amphotericin B Amfotericine B
|
||||||
nl Aldesulfone sodium Aldesulfon TRUE FALSE FALSE
|
nl Ampicillin Ampicilline
|
||||||
nl Amikacin Amikacine TRUE FALSE FALSE
|
nl Ampicillin/beta-lactamase inhibitor Ampicilline/enzymremmer
|
||||||
nl Amoxicillin Amoxicilline TRUE FALSE FALSE
|
nl Anidulafungin Anidulafungine
|
||||||
nl Amoxicillin/beta-lactamase inhibitor Amoxicilline/enzymremmer TRUE FALSE FALSE
|
nl Azidocillin Azidocilline
|
||||||
nl Amphotericin B Amfotericine B TRUE FALSE FALSE
|
nl Azithromycin Azitromycine
|
||||||
nl Ampicillin Ampicilline TRUE FALSE FALSE
|
nl Azlocillin Azlocilline
|
||||||
nl Ampicillin/beta-lactamase inhibitor Ampicilline/enzymremmer TRUE FALSE FALSE
|
nl Bacampicillin Bacampicilline
|
||||||
nl Anidulafungin Anidulafungine TRUE FALSE FALSE
|
nl Bacitracin Bacitracine
|
||||||
nl Azidocillin Azidocilline TRUE FALSE FALSE
|
nl Benzathine benzylpenicillin Benzylpenicillinebenzathine
|
||||||
nl Azithromycin Azitromycine TRUE FALSE FALSE
|
nl Benzathine phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine
|
||||||
nl Azlocillin Azlocilline TRUE FALSE FALSE
|
nl Benzylpenicillin Benzylpenicilline
|
||||||
nl Bacampicillin Bacampicilline TRUE FALSE FALSE
|
nl Calcium aminosalicylate Aminosalicylzuur
|
||||||
nl Bacitracin Bacitracine TRUE FALSE FALSE
|
nl Capreomycin Capreomycine
|
||||||
nl Benzathine benzylpenicillin Benzylpenicillinebenzathine TRUE FALSE FALSE
|
nl Carbenicillin Carbenicilline
|
||||||
nl Benzathine phenoxymethylpenicillin Fenoxymethylpenicillinebenzathine TRUE FALSE FALSE
|
nl Carindacillin Carindacilline
|
||||||
nl Benzylpenicillin Benzylpenicilline TRUE FALSE FALSE
|
nl Caspofungin Caspofungine
|
||||||
nl Calcium aminosalicylate Aminosalicylzuur TRUE FALSE FALSE
|
nl Ce(f|ph)acetrile Cefacetril FALSE
|
||||||
nl Capreomycin Capreomycine TRUE FALSE FALSE
|
nl Ce(f|ph)alexin Cefalexine FALSE FALSE
|
||||||
nl Carbenicillin Carbenicilline TRUE FALSE FALSE
|
nl Ce(f|ph)alotin Cefalotine FALSE
|
||||||
nl Carindacillin Carindacilline TRUE FALSE FALSE
|
nl Ce(f|ph)amandole Cefamandol FALSE
|
||||||
nl Caspofungin Caspofungine TRUE FALSE FALSE
|
nl Ce(f|ph)apirin Cefapirine FALSE
|
||||||
nl Ce(f|ph)acetrile Cefacetril FALSE FALSE FALSE
|
nl Ce(f|ph)azedone Cefazedon FALSE
|
||||||
nl Ce(f|ph)alexin Cefalexine FALSE FALSE FALSE
|
nl Ce(f|ph)azolin Cefazoline FALSE
|
||||||
nl Ce(f|ph)alotin Cefalotine FALSE FALSE FALSE
|
nl Ce(f|ph)alothin Cefalotine FALSE
|
||||||
nl Ce(f|ph)amandole Cefamandol FALSE FALSE FALSE
|
nl Ce(f|ph)alexin Cefalexine FALSE
|
||||||
nl Ce(f|ph)apirin Cefapirine FALSE FALSE FALSE
|
nl Ce(f|ph)epime Cefepim FALSE
|
||||||
nl Ce(f|ph)azedone Cefazedon FALSE FALSE FALSE
|
nl Ce(f|ph)ixime Cefixim FALSE
|
||||||
nl Ce(f|ph)azolin Cefazoline FALSE FALSE FALSE
|
nl Ce(f|ph)menoxime Cefmenoxim FALSE
|
||||||
nl Ce(f|ph)alothin Cefalotine FALSE FALSE FALSE
|
nl Ce(f|ph)metazole Cefmetazol FALSE
|
||||||
nl Ce(f|ph)alexin Cefalexine FALSE FALSE FALSE
|
nl Ce(f|ph)odizime Cefodizim FALSE
|
||||||
nl Ce(f|ph)epime Cefepim FALSE FALSE FALSE
|
nl Ce(f|ph)onicid Cefonicide FALSE
|
||||||
nl Ce(f|ph)ixime Cefixim FALSE FALSE FALSE
|
nl Ce(f|ph)operazone Cefoperazon FALSE
|
||||||
nl Ce(f|ph)menoxime Cefmenoxim FALSE FALSE FALSE
|
nl Ce(f|ph)operazone/beta-lactamase inhibitor Cefoperazon/enzymremmer FALSE
|
||||||
nl Ce(f|ph)metazole Cefmetazol FALSE FALSE FALSE
|
nl Ce(f|ph)otaxime Cefotaxim FALSE
|
||||||
nl Ce(f|ph)odizime Cefodizim FALSE FALSE FALSE
|
nl Ce(f|ph)oxitin Cefoxitine FALSE
|
||||||
nl Ce(f|ph)onicid Cefonicide FALSE FALSE FALSE
|
nl Ce(f|ph)pirome Cefpirom FALSE
|
||||||
nl Ce(f|ph)operazone Cefoperazon FALSE FALSE FALSE
|
nl Ce(f|ph)podoxime Cefpodoxim FALSE
|
||||||
nl Ce(f|ph)operazone/beta-lactamase inhibitor Cefoperazon/enzymremmer FALSE FALSE FALSE
|
nl Ce(f|ph)radine Cefradine FALSE
|
||||||
nl Ce(f|ph)otaxime Cefotaxim FALSE FALSE FALSE
|
nl Ce(f|ph)sulodin Cefsulodine FALSE
|
||||||
nl Ce(f|ph)oxitin Cefoxitine FALSE FALSE FALSE
|
nl Ce(f|ph)tazidime Ceftazidim FALSE
|
||||||
nl Ce(f|ph)pirome Cefpirom FALSE FALSE FALSE
|
nl Ce(f|ph)tezole Ceftezol FALSE
|
||||||
nl Ce(f|ph)podoxime Cefpodoxim FALSE FALSE FALSE
|
nl Ce(f|ph)tizoxime Ceftizoxim FALSE
|
||||||
nl Ce(f|ph)radine Cefradine FALSE FALSE FALSE
|
nl Ce(f|ph)triaxone Ceftriaxon FALSE
|
||||||
nl Ce(f|ph)sulodin Cefsulodine FALSE FALSE FALSE
|
nl Ce(f|ph)uroxime Cefuroxim FALSE
|
||||||
nl Ce(f|ph)tazidime Ceftazidim FALSE FALSE FALSE
|
nl Ce(f|ph)uroxime/metronidazole Cefuroxim/andere antibacteriele middelen FALSE
|
||||||
nl Ce(f|ph)tezole Ceftezol FALSE FALSE FALSE
|
nl Chloramphenicol Chlooramfenicol
|
||||||
nl Ce(f|ph)tizoxime Ceftizoxim FALSE FALSE FALSE
|
nl Chlortetracycline Chloortetracycline
|
||||||
nl Ce(f|ph)triaxone Ceftriaxon FALSE FALSE FALSE
|
nl Cinoxacin Cinoxacine
|
||||||
nl Ce(f|ph)uroxime Cefuroxim FALSE FALSE FALSE
|
nl Ciprofloxacin Ciprofloxacine
|
||||||
nl Ce(f|ph)uroxime/metronidazole Cefuroxim/andere antibacteriele middelen FALSE FALSE FALSE
|
nl Clarithromycin Claritromycine
|
||||||
nl Chloramphenicol Chlooramfenicol TRUE FALSE FALSE
|
nl Clavulanic acid Clavulaanzuur
|
||||||
nl Chlortetracycline Chloortetracycline TRUE FALSE FALSE
|
nl clavulanic acid clavulaanzuur
|
||||||
nl Cinoxacin Cinoxacine TRUE FALSE FALSE
|
nl Clindamycin Clindamycine
|
||||||
nl Ciprofloxacin Ciprofloxacine TRUE FALSE FALSE
|
nl Clometocillin Clometocilline
|
||||||
nl Clarithromycin Claritromycine TRUE FALSE FALSE
|
nl Clotrimazole Clotrimazol
|
||||||
nl Clavulanic acid Clavulaanzuur TRUE FALSE FALSE
|
nl Cloxacillin Cloxacilline
|
||||||
nl clavulanic acid clavulaanzuur TRUE FALSE FALSE
|
nl Colistin Colistine
|
||||||
nl Clindamycin Clindamycine TRUE FALSE FALSE
|
nl Dapsone Dapson
|
||||||
nl Clometocillin Clometocilline TRUE FALSE FALSE
|
nl Daptomycin Daptomycine
|
||||||
nl Clotrimazole Clotrimazol TRUE FALSE FALSE
|
nl Dibekacin Dibekacine
|
||||||
nl Cloxacillin Cloxacilline TRUE FALSE FALSE
|
nl Dicloxacillin Dicloxacilline
|
||||||
nl Colistin Colistine TRUE FALSE FALSE
|
nl Dirithromycin Diritromycine
|
||||||
nl Dapsone Dapson TRUE FALSE FALSE
|
nl Econazole Econazol
|
||||||
nl Daptomycin Daptomycine TRUE FALSE FALSE
|
nl Enoxacin Enoxacine
|
||||||
nl Dibekacin Dibekacine TRUE FALSE FALSE
|
nl Epicillin Epicilline
|
||||||
nl Dicloxacillin Dicloxacilline TRUE FALSE FALSE
|
nl Erythromycin Erytromycine
|
||||||
nl Dirithromycin Diritromycine TRUE FALSE FALSE
|
nl Ethambutol/isoniazid Ethambutol/isoniazide
|
||||||
nl Econazole Econazol TRUE FALSE FALSE
|
nl Fleroxacin Fleroxacine
|
||||||
nl Enoxacin Enoxacine TRUE FALSE FALSE
|
nl Flucloxacillin Flucloxacilline
|
||||||
nl Epicillin Epicilline TRUE FALSE FALSE
|
nl Fluconazole Fluconazol
|
||||||
nl Erythromycin Erytromycine TRUE FALSE FALSE
|
nl Flucytosine Fluorocytosine
|
||||||
nl Ethambutol/isoniazid Ethambutol/isoniazide TRUE FALSE FALSE
|
nl Flurithromycin Fluritromycine
|
||||||
nl Fleroxacin Fleroxacine TRUE FALSE FALSE
|
nl Fosfomycin Fosfomycine
|
||||||
nl Flucloxacillin Flucloxacilline TRUE FALSE FALSE
|
nl Fusidic acid Fusidinezuur
|
||||||
nl Fluconazole Fluconazol TRUE FALSE FALSE
|
nl Gatifloxacin Gatifloxacine
|
||||||
nl Flucytosine Fluorocytosine TRUE FALSE FALSE
|
nl Gemifloxacin Gemifloxacine
|
||||||
nl Flurithromycin Fluritromycine TRUE FALSE FALSE
|
nl Gentamicin Gentamicine
|
||||||
nl Fosfomycin Fosfomycine TRUE FALSE FALSE
|
nl Grepafloxacin Grepafloxacine
|
||||||
nl Fusidic acid Fusidinezuur TRUE FALSE FALSE
|
nl Hachimycin Hachimycine
|
||||||
nl Gatifloxacin Gatifloxacine TRUE FALSE FALSE
|
nl Hetacillin Hetacilline
|
||||||
nl Gemifloxacin Gemifloxacine TRUE FALSE FALSE
|
nl Imipenem/cilastatin Imipenem/enzymremmer
|
||||||
nl Gentamicin Gentamicine TRUE FALSE FALSE
|
nl Inosine pranobex Inosiplex
|
||||||
nl Grepafloxacin Grepafloxacine TRUE FALSE FALSE
|
nl Isepamicin Isepamicine
|
||||||
nl Hachimycin Hachimycine TRUE FALSE FALSE
|
nl Isoconazole Isoconazol
|
||||||
nl Hetacillin Hetacilline TRUE FALSE FALSE
|
nl Isoniazid Isoniazide
|
||||||
nl Imipenem/cilastatin Imipenem/enzymremmer TRUE FALSE FALSE
|
nl Itraconazole Itraconazol
|
||||||
nl Inosine pranobex Inosiplex TRUE FALSE FALSE
|
nl Josamycin Josamycine
|
||||||
nl Isepamicin Isepamicine TRUE FALSE FALSE
|
nl Kanamycin Kanamycine
|
||||||
nl Isoconazole Isoconazol TRUE FALSE FALSE
|
nl Ketoconazole Ketoconazol
|
||||||
nl Isoniazid Isoniazide TRUE FALSE FALSE
|
nl Levofloxacin Levofloxacine
|
||||||
nl Itraconazole Itraconazol TRUE FALSE FALSE
|
nl Lincomycin Lincomycine
|
||||||
nl Josamycin Josamycine TRUE FALSE FALSE
|
nl Lomefloxacin Lomefloxacine
|
||||||
nl Kanamycin Kanamycine TRUE FALSE FALSE
|
nl Lysozyme Lysozym
|
||||||
nl Ketoconazole Ketoconazol TRUE FALSE FALSE
|
nl Mandelic acid Amandelzuur
|
||||||
nl Levofloxacin Levofloxacine TRUE FALSE FALSE
|
nl Metampicillin Metampicilline
|
||||||
nl Lincomycin Lincomycine TRUE FALSE FALSE
|
nl Meticillin Meticilline
|
||||||
nl Lomefloxacin Lomefloxacine TRUE FALSE FALSE
|
nl Metisazone Metisazon
|
||||||
nl Lysozyme Lysozym TRUE FALSE FALSE
|
nl Metronidazole Metronidazol
|
||||||
nl Mandelic acid Amandelzuur TRUE FALSE FALSE
|
nl Mezlocillin Mezlocilline
|
||||||
nl Metampicillin Metampicilline TRUE FALSE FALSE
|
nl Micafungin Micafungine
|
||||||
nl Meticillin Meticilline TRUE FALSE FALSE
|
nl Miconazole Miconazol
|
||||||
nl Metisazone Metisazon TRUE FALSE FALSE
|
nl Midecamycin Midecamycine
|
||||||
nl Metronidazole Metronidazol TRUE FALSE FALSE
|
nl Miocamycin Miocamycine
|
||||||
nl Mezlocillin Mezlocilline TRUE FALSE FALSE
|
nl Moxifloxacin Moxifloxacine
|
||||||
nl Micafungin Micafungine TRUE FALSE FALSE
|
nl Mupirocin Mupirocine
|
||||||
nl Miconazole Miconazol TRUE FALSE FALSE
|
nl Nalidixic acid Nalidixinezuur
|
||||||
nl Midecamycin Midecamycine TRUE FALSE FALSE
|
nl Neomycin Neomycine
|
||||||
nl Miocamycin Miocamycine TRUE FALSE FALSE
|
nl Netilmicin Netilmicine
|
||||||
nl Moxifloxacin Moxifloxacine TRUE FALSE FALSE
|
nl Nitrofurantoin Nitrofurantoine
|
||||||
nl Mupirocin Mupirocine TRUE FALSE FALSE
|
nl Norfloxacin Norfloxacine
|
||||||
nl Nalidixic acid Nalidixinezuur TRUE FALSE FALSE
|
nl Novobiocin Novobiocine
|
||||||
nl Neomycin Neomycine TRUE FALSE FALSE
|
nl Nystatin Nystatine
|
||||||
nl Netilmicin Netilmicine TRUE FALSE FALSE
|
nl Ofloxacin Ofloxacine
|
||||||
nl Nitrofurantoin Nitrofurantoine TRUE FALSE FALSE
|
nl Oleandomycin Oleandomycine
|
||||||
nl Norfloxacin Norfloxacine TRUE FALSE FALSE
|
nl Ornidazole Ornidazol
|
||||||
nl Novobiocin Novobiocine TRUE FALSE FALSE
|
nl Oxacillin Oxacilline
|
||||||
nl Nystatin Nystatine TRUE FALSE FALSE
|
nl Oxolinic acid Oxolinezuur
|
||||||
nl Ofloxacin Ofloxacine TRUE FALSE FALSE
|
nl Oxytetracycline Oxytetracycline
|
||||||
nl Oleandomycin Oleandomycine TRUE FALSE FALSE
|
nl Pazufloxacin Pazufloxacine
|
||||||
nl Ornidazole Ornidazol TRUE FALSE FALSE
|
nl Pefloxacin Pefloxacine
|
||||||
nl Oxacillin Oxacilline TRUE FALSE FALSE
|
nl Penamecillin Penamecilline
|
||||||
nl Oxolinic acid Oxolinezuur TRUE FALSE FALSE
|
nl Penicillin Penicilline
|
||||||
nl Oxytetracycline Oxytetracycline TRUE FALSE FALSE
|
nl Pheneticillin Feneticilline
|
||||||
nl Pazufloxacin Pazufloxacine TRUE FALSE FALSE
|
nl Phenoxymethylpenicillin Fenoxymethylpenicilline
|
||||||
nl Pefloxacin Pefloxacine TRUE FALSE FALSE
|
nl Pipemidic acid Pipemidinezuur
|
||||||
nl Penamecillin Penamecilline TRUE FALSE FALSE
|
nl Piperacillin Piperacilline
|
||||||
nl Penicillin Penicilline TRUE FALSE FALSE
|
nl Piperacillin/beta-lactamase inhibitor Piperacilline/enzymremmer
|
||||||
nl Pheneticillin Feneticilline TRUE FALSE FALSE
|
nl Piromidic acid Piromidinezuur
|
||||||
nl Phenoxymethylpenicillin Fenoxymethylpenicilline TRUE FALSE FALSE
|
nl Pivampicillin Pivampicilline
|
||||||
nl Pipemidic acid Pipemidinezuur TRUE FALSE FALSE
|
nl Polymyxin B Polymyxine B
|
||||||
nl Piperacillin Piperacilline TRUE FALSE FALSE
|
nl Posaconazole Posaconazol
|
||||||
nl Piperacillin/beta-lactamase inhibitor Piperacilline/enzymremmer TRUE FALSE FALSE
|
nl Pristinamycin Pristinamycine
|
||||||
nl Piromidic acid Piromidinezuur TRUE FALSE FALSE
|
nl Procaine benzylpenicillin Benzylpenicillineprocaine
|
||||||
nl Pivampicillin Pivampicilline TRUE FALSE FALSE
|
nl Propicillin Propicilline
|
||||||
nl Polymyxin B Polymyxine B TRUE FALSE FALSE
|
nl Prulifloxacin Prulifloxacine
|
||||||
nl Posaconazole Posaconazol TRUE FALSE FALSE
|
nl Quinupristin/dalfopristin Quinupristine/dalfopristine
|
||||||
nl Pristinamycin Pristinamycine TRUE FALSE FALSE
|
nl Ribostamycin Ribostamycine
|
||||||
nl Procaine benzylpenicillin Benzylpenicillineprocaine TRUE FALSE FALSE
|
nl Rifabutin Rifabutine
|
||||||
nl Propicillin Propicilline TRUE FALSE FALSE
|
nl Rifampicin Rifampicine
|
||||||
nl Prulifloxacin Prulifloxacine TRUE FALSE FALSE
|
nl Rifampicin/pyrazinamide/ethambutol/isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide
|
||||||
nl Quinupristin/dalfopristin Quinupristine/dalfopristine TRUE FALSE FALSE
|
nl Rifampicin/pyrazinamide/isoniazid Rifampicine/pyrazinamide/isoniazide
|
||||||
nl Ribostamycin Ribostamycine TRUE FALSE FALSE
|
nl Rifampicin/isoniazid Rifampicine/isoniazide
|
||||||
nl Rifabutin Rifabutine TRUE FALSE FALSE
|
nl Rifamycin Rifamycine
|
||||||
nl Rifampicin Rifampicine TRUE FALSE FALSE
|
nl Rifaximin Rifaximine
|
||||||
nl Rifampicin/pyrazinamide/ethambutol/isoniazid Rifampicine/pyrazinamide/ethambutol/isoniazide TRUE FALSE FALSE
|
nl Rokitamycin Rokitamycine
|
||||||
nl Rifampicin/pyrazinamide/isoniazid Rifampicine/pyrazinamide/isoniazide TRUE FALSE FALSE
|
nl Rosoxacin Rosoxacine
|
||||||
nl Rifampicin/isoniazid Rifampicine/isoniazide TRUE FALSE FALSE
|
nl Roxithromycin Roxitromycine
|
||||||
nl Rifamycin Rifamycine TRUE FALSE FALSE
|
nl Rufloxacin Rufloxacine
|
||||||
nl Rifaximin Rifaximine TRUE FALSE FALSE
|
nl Sisomicin Sisomicine
|
||||||
nl Rokitamycin Rokitamycine TRUE FALSE FALSE
|
nl Sodium aminosalicylate Aminosalicylzuur
|
||||||
nl Rosoxacin Rosoxacine TRUE FALSE FALSE
|
nl Sparfloxacin Sparfloxacine
|
||||||
nl Roxithromycin Roxitromycine TRUE FALSE FALSE
|
nl Spectinomycin Spectinomycine
|
||||||
nl Rufloxacin Rufloxacine TRUE FALSE FALSE
|
nl Spiramycin Spiramycine
|
||||||
nl Sisomicin Sisomicine TRUE FALSE FALSE
|
nl Spiramycin/metronidazole Spiramycine/metronidazol
|
||||||
nl Sodium aminosalicylate Aminosalicylzuur TRUE FALSE FALSE
|
nl Staphylococcus immunoglobulin Stafylokokkenimmunoglobuline
|
||||||
nl Sparfloxacin Sparfloxacine TRUE FALSE FALSE
|
nl Streptoduocin Streptoduocine
|
||||||
nl Spectinomycin Spectinomycine TRUE FALSE FALSE
|
nl Streptomycin Streptomycine
|
||||||
nl Spiramycin Spiramycine TRUE FALSE FALSE
|
nl Streptomycin/isoniazid Streptomycine/isoniazide
|
||||||
nl Spiramycin/metronidazole Spiramycine/metronidazol TRUE FALSE FALSE
|
nl Sulbenicillin Sulbenicilline
|
||||||
nl Staphylococcus immunoglobulin Stafylokokkenimmunoglobuline TRUE FALSE FALSE
|
nl Sulfadiazine/tetroxoprim Sulfadiazine/tetroxoprim
|
||||||
nl Streptoduocin Streptoduocine TRUE FALSE FALSE
|
nl Sulfadiazine/trimethoprim Sulfadiazine/trimethoprim
|
||||||
nl Streptomycin Streptomycine TRUE FALSE FALSE
|
nl Sulfadimidine/trimethoprim Sulfadimidine/trimethoprim
|
||||||
nl Streptomycin/isoniazid Streptomycine/isoniazide TRUE FALSE FALSE
|
nl Sulfafurazole Sulfafurazol
|
||||||
nl Sulbenicillin Sulbenicilline TRUE FALSE FALSE
|
nl Sulfaisodimidine Sulfisomidine
|
||||||
nl Sulfadiazine/tetroxoprim Sulfadiazine/tetroxoprim TRUE FALSE FALSE
|
nl Sulfalene Sulfaleen
|
||||||
nl Sulfadiazine/trimethoprim Sulfadiazine/trimethoprim TRUE FALSE FALSE
|
nl Sulfamazone Sulfamazon
|
||||||
nl Sulfadimidine/trimethoprim Sulfadimidine/trimethoprim TRUE FALSE FALSE
|
nl Sulfamerazine/trimethoprim Sulfamerazine/trimethoprim
|
||||||
nl Sulfafurazole Sulfafurazol TRUE FALSE FALSE
|
nl Sulfamethizole Sulfamethizol
|
||||||
nl Sulfaisodimidine Sulfisomidine TRUE FALSE FALSE
|
nl Sulfamethoxazole Sulfamethoxazol
|
||||||
nl Sulfalene Sulfaleen TRUE FALSE FALSE
|
nl Sulfamethoxazole/trimethoprim Sulfamethoxazol/trimethoprim
|
||||||
nl Sulfamazone Sulfamazon TRUE FALSE FALSE
|
nl Sulfametoxydiazine Sulfamethoxydiazine
|
||||||
nl Sulfamerazine/trimethoprim Sulfamerazine/trimethoprim TRUE FALSE FALSE
|
nl Sulfametrole/trimethoprim Sulfametrol/trimethoprim
|
||||||
nl Sulfamethizole Sulfamethizol TRUE FALSE FALSE
|
nl Sulfamoxole Sulfamoxol
|
||||||
nl Sulfamethoxazole Sulfamethoxazol TRUE FALSE FALSE
|
nl Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim
|
||||||
nl Sulfamethoxazole/trimethoprim Sulfamethoxazol/trimethoprim TRUE FALSE FALSE
|
nl Sulfaperin Sulfaperine
|
||||||
nl Sulfametoxydiazine Sulfamethoxydiazine TRUE FALSE FALSE
|
nl Sulfaphenazole Sulfafenazol
|
||||||
nl Sulfametrole/trimethoprim Sulfametrol/trimethoprim TRUE FALSE FALSE
|
nl Sulfathiazole Sulfathiazol
|
||||||
nl Sulfamoxole Sulfamoxol TRUE FALSE FALSE
|
nl Sulfathiourea Sulfathioureum
|
||||||
nl Sulfamoxole/trimethoprim Sulfamoxol/trimethoprim TRUE FALSE FALSE
|
nl Sultamicillin Sultamicilline
|
||||||
nl Sulfaperin Sulfaperine TRUE FALSE FALSE
|
nl Talampicillin Talampicilline
|
||||||
nl Sulfaphenazole Sulfafenazol TRUE FALSE FALSE
|
nl Teicoplanin Teicoplanine
|
||||||
nl Sulfathiazole Sulfathiazol TRUE FALSE FALSE
|
nl Telithromycin Telitromycine
|
||||||
nl Sulfathiourea Sulfathioureum TRUE FALSE FALSE
|
nl Temafloxacin Temafloxacine
|
||||||
nl Sultamicillin Sultamicilline TRUE FALSE FALSE
|
nl Temocillin Temocilline
|
||||||
nl Talampicillin Talampicilline TRUE FALSE FALSE
|
nl Tenofovir disoproxil Tenofovir
|
||||||
nl Teicoplanin Teicoplanine TRUE FALSE FALSE
|
nl Terizidone Terizidon
|
||||||
nl Telithromycin Telitromycine TRUE FALSE FALSE
|
nl Thiamphenicol Thiamfenicol
|
||||||
nl Temafloxacin Temafloxacine TRUE FALSE FALSE
|
nl Thioacetazone/isoniazid Thioacetazon/isoniazide
|
||||||
nl Temocillin Temocilline TRUE FALSE FALSE
|
nl Ticarcillin Ticarcilline
|
||||||
nl Tenofovir disoproxil Tenofovir TRUE FALSE FALSE
|
nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer
|
||||||
nl Terizidone Terizidon TRUE FALSE FALSE
|
nl Ticarcillin/clavulanic acid Ticarcilline/clavulaanzuur
|
||||||
nl Thiamphenicol Thiamfenicol TRUE FALSE FALSE
|
nl Tinidazole Tinidazol
|
||||||
nl Thioacetazone/isoniazid Thioacetazon/isoniazide TRUE FALSE FALSE
|
nl Tobramycin Tobramycine
|
||||||
nl Ticarcillin Ticarcilline TRUE FALSE FALSE
|
nl Trimethoprim/sulfamethoxazole Cotrimoxazol
|
||||||
nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer TRUE FALSE FALSE
|
nl Troleandomycin Troleandomycine
|
||||||
nl Ticarcillin/clavulanic acid Ticarcilline/clavulaanzuur TRUE FALSE FALSE
|
nl Trovafloxacin Trovafloxacine
|
||||||
nl Tinidazole Tinidazol TRUE FALSE FALSE
|
nl Vancomycin Vancomycine
|
||||||
nl Tobramycin Tobramycine TRUE FALSE FALSE
|
nl Voriconazole Voriconazol
|
||||||
nl Trimethoprim/sulfamethoxazole Cotrimoxazol TRUE FALSE FALSE
|
nl Aminoglycosides Aminoglycosiden TRUE FALSE
|
||||||
nl Troleandomycin Troleandomycine TRUE FALSE FALSE
|
nl Amphenicols Amfenicolen TRUE FALSE
|
||||||
nl Trovafloxacin Trovafloxacine TRUE FALSE FALSE
|
nl Antifungals/antimycotics Antifungica/antimycotica TRUE FALSE
|
||||||
nl Vancomycin Vancomycine TRUE FALSE FALSE
|
nl Antimycobacterials Antimycobacteriele middelen TRUE FALSE
|
||||||
nl Voriconazole Voriconazol TRUE FALSE FALSE
|
nl Beta-lactams/penicillins Beta-lactams/penicillines TRUE FALSE
|
||||||
nl Aminoglycosides Aminoglycosiden TRUE FALSE FALSE
|
nl Cephalosporins (1st gen.) Cefalosporines (1e gen.) TRUE FALSE
|
||||||
nl Amphenicols Amfenicolen TRUE FALSE FALSE
|
nl Cephalosporins (2nd gen.) Cefalosporines (2e gen.) TRUE FALSE
|
||||||
nl Antifungals/antimycotics Antifungica/antimycotica TRUE FALSE FALSE
|
nl Cephalosporins (3rd gen.) Cefalosporines (3e gen.) TRUE FALSE
|
||||||
nl Antimycobacterials Antimycobacteriele middelen TRUE FALSE FALSE
|
nl Cephalosporins (4th gen.) Cefalosporines (4e gen.) TRUE FALSE
|
||||||
nl Beta-lactams/penicillins Beta-lactams/penicillines TRUE FALSE FALSE
|
nl Cephalosporins (5th gen.) Cefalosporines (5e gen.) TRUE FALSE
|
||||||
nl Cephalosporins (1st gen.) Cefalosporines (1e gen.) TRUE FALSE FALSE
|
nl Cephalosporins (unclassified gen.) Cefalosporines (ongeclassificeerd) TRUE FALSE
|
||||||
nl Cephalosporins (2nd gen.) Cefalosporines (2e gen.) TRUE FALSE FALSE
|
nl Cephalosporins Cefalosporines TRUE FALSE
|
||||||
nl Cephalosporins (3rd gen.) Cefalosporines (3e gen.) TRUE FALSE FALSE
|
nl Glycopeptides Glycopeptiden TRUE FALSE
|
||||||
nl Cephalosporins (4th gen.) Cefalosporines (4e gen.) TRUE FALSE FALSE
|
nl Macrolides/lincosamides Macroliden/lincosamiden TRUE FALSE
|
||||||
nl Cephalosporins (5th gen.) Cefalosporines (5e gen.) TRUE FALSE FALSE
|
nl Other antibacterials Overige antibiotica TRUE FALSE
|
||||||
nl Cephalosporins (unclassified gen.) Cefalosporines (ongeclassificeerd) TRUE FALSE FALSE
|
nl Polymyxins Polymyxines TRUE FALSE
|
||||||
nl Cephalosporins Cefalosporines TRUE FALSE FALSE
|
nl Quinolones Quinolonen TRUE FALSE
|
||||||
nl Glycopeptides Glycopeptiden TRUE FALSE FALSE
|
|
||||||
nl Macrolides/lincosamides Macroliden/lincosamiden TRUE FALSE FALSE
|
|
||||||
nl Other antibacterials Overige antibiotica TRUE FALSE FALSE
|
|
||||||
nl Polymyxins Polymyxines TRUE FALSE FALSE
|
|
||||||
nl Quinolones Quinolonen TRUE FALSE FALSE
|
|
||||||
|
|||||||
|
Can't render this file because it has a wrong number of fields in line 186.
|
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
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|
||||||
|
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
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|
||||||
|
|
||||||
|
|||||||
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|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
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|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -88,7 +88,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
|
|||||||
/* adjusted colour for all real links; having href attribute */
|
/* adjusted colour for all real links; having href attribute */
|
||||||
color: #128f76;
|
color: #128f76;
|
||||||
}
|
}
|
||||||
.ot, .dv, .fl, .cn {
|
.ot, .dv {
|
||||||
/* numbers and TRUE/FALSE */
|
/* numbers and TRUE/FALSE */
|
||||||
color: slategray;
|
color: slategray;
|
||||||
}
|
}
|
||||||
@ -187,13 +187,10 @@ div[id^=last-updated] h2 {
|
|||||||
}
|
}
|
||||||
|
|
||||||
/* tables, make them look like scientific ones */
|
/* tables, make them look like scientific ones */
|
||||||
table {
|
.table {
|
||||||
font-size: 90%;
|
font-size: 90%;
|
||||||
}
|
}
|
||||||
table * {
|
.table td {
|
||||||
vertical-align: middle !important;
|
|
||||||
}
|
|
||||||
table td {
|
|
||||||
padding: 4px !important;
|
padding: 4px !important;
|
||||||
}
|
}
|
||||||
thead {
|
thead {
|
||||||
|
|||||||
@ -43,7 +43,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -395,9 +395,8 @@ Since you are one of our users, we would like to know how you use the package an
|
|||||||
<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
|
<p><img src="https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master" alt="R-code-check"><a href="https://www.codefactor.io/repository/github/msberends/amr"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=master"><img src="https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg" alt="Codecov"></a></p>
|
||||||
<p>The latest and unpublished development version can be installed from GitHub using:</p>
|
<p>The latest and unpublished development version can be installed from GitHub using:</p>
|
||||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span>
|
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span>
|
||||||
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
|
<span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></code></pre></div>
|
||||||
<p>You can also download the latest build from our repository: <a href="https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz" class="uri">https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz</a></p>
|
|
||||||
</div>
|
</div>
|
||||||
</div>
|
</div>
|
||||||
<div id="get-started" class="section level3">
|
<div id="get-started" class="section level3">
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -236,13 +236,13 @@
|
|||||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-1509020" class="section level1">
|
<div id="amr-1509018" class="section level1">
|
||||||
<h1 class="page-header" data-toc-text="1.5.0.9020">
|
<h1 class="page-header" data-toc-text="1.5.0.9018">
|
||||||
<a href="#amr-1509020" class="anchor"></a>AMR 1.5.0.9020<small> Unreleased </small>
|
<a href="#amr-1509018" class="anchor"></a>AMR 1.5.0.9018<small> Unreleased </small>
|
||||||
</h1>
|
</h1>
|
||||||
<div id="last-updated-18-february-2021" class="section level2">
|
<div id="last-updated-9-february-2021" class="section level2">
|
||||||
<h2 class="hasAnchor">
|
<h2 class="hasAnchor">
|
||||||
<a href="#last-updated-18-february-2021" class="anchor"></a><small>Last updated: 18 February 2021</small>
|
<a href="#last-updated-9-february-2021" class="anchor"></a><small>Last updated: 9 February 2021</small>
|
||||||
</h2>
|
</h2>
|
||||||
<div id="new" class="section level3">
|
<div id="new" class="section level3">
|
||||||
<h3 class="hasAnchor">
|
<h3 class="hasAnchor">
|
||||||
@ -259,11 +259,11 @@
|
|||||||
<li>
|
<li>
|
||||||
<p>Added argument <code>only_rsi_columns</code> for some functions, which defaults to <code>FALSE</code>, to indicate if the functions must only be applied to columns that are of class <code><rsi></code> (i.e., transformed with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:</p>
|
<p>Added argument <code>only_rsi_columns</code> for some functions, which defaults to <code>FALSE</code>, to indicate if the functions must only be applied to columns that are of class <code><rsi></code> (i.e., transformed with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>). This increases speed since automatic determination of antibiotic columns is not needed anymore. Affected functions are:</p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>All antibiotic selector functions (<code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
|
<li>All antibiotic selector functions (<code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code> and its wrappers, such as <code>aminoglocysides()</code>, <code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>)</li>
|
||||||
<li>All antibiotic filter functions (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code><a href="../reference/filter_ab_class.html">filter_aminoglycosides()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
|
<li>All antibiotic filter functions (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code> and its wrappers, such as <code>filter_aminoglocysides()</code>, <code><a href="../reference/filter_ab_class.html">filter_carbapenems()</a></code>, <code><a href="../reference/filter_ab_class.html">filter_penicillins()</a></code>)</li>
|
||||||
<li><code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></li>
|
<li><code><a href="../reference/eucast_rules.html">eucast_rules()</a></code></li>
|
||||||
<li>
|
<li>
|
||||||
<code><a href="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code> and <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
|
<code><a href="../reference/mdro.html">mdro()</a></code> (including wrappers such as <code><a href="../reference/mdro.html">brmo()</a></code>, <code>mrgn</code> and <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>)</li>
|
||||||
<li><code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code></li>
|
<li><code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code></li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
@ -325,7 +325,6 @@
|
|||||||
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
|
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
||||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
|
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
<div id="other" class="section level3">
|
<div id="other" class="section level3">
|
||||||
@ -652,7 +651,7 @@
|
|||||||
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) 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.</p>
|
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) 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.</p>
|
||||||
<p>Negative effects of this change are:</p>
|
<p>Negative effects of this change are:</p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
|
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
|
||||||
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
||||||
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
||||||
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
||||||
@ -989,7 +988,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
|
<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
|
||||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||||
</li>
|
</li>
|
||||||
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
@ -1258,7 +1257,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
|
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
|
||||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>Frequency tables (<code>freq()</code>):
|
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
|
||||||
<ul>
|
<ul>
|
||||||
<li><p>speed improvement for microbial IDs</p></li>
|
<li><p>speed improvement for microbial IDs</p></li>
|
||||||
<li><p>fixed factor level names for R Markdown</p></li>
|
<li><p>fixed factor level names for R Markdown</p></li>
|
||||||
@ -1268,12 +1267,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R">
|
<code class="sourceCode R">
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||||
<span class="co"># grouped boxplots:</span>
|
<span class="co"># grouped boxplots:</span>
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
@ -1283,7 +1282,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||||
</li>
|
</li>
|
||||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
||||||
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
|
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
|
||||||
</li>
|
</li>
|
||||||
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
||||||
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
||||||
@ -1524,7 +1523,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</li>
|
</li>
|
||||||
<li>Frequency tables (<code>freq()</code> function):
|
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
|
||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||||
@ -1534,15 +1533,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<span class="co"># OLD WAY</span>
|
<span class="co"># OLD WAY</span>
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||||
<span class="co"># NEW WAY</span>
|
<span class="co"># NEW WAY</span>
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||||
|
|
||||||
<span class="co"># Even supports grouping variables:</span>
|
<span class="co"># Even supports grouping variables:</span>
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||||
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||||
@ -1625,7 +1624,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
|
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
|
||||||
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
|
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
|
||||||
<li>
|
<li>
|
||||||
<p>Frequency tables - <code>freq()</code>:</p>
|
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
|
||||||
<ul>
|
<ul>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for grouping variables, test with:</p>
|
<p>Support for grouping variables, test with:</p>
|
||||||
@ -1633,14 +1632,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<code class="sourceCode R">
|
<code class="sourceCode R">
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li>
|
<li>
|
||||||
<p>Support for (un)selecting columns:</p>
|
<p>Support for (un)selecting columns:</p>
|
||||||
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R">
|
<code class="sourceCode R">
|
||||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||||
@ -1658,7 +1657,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
|
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
|
||||||
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
|
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
|
||||||
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
|
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
|
||||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
|
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
|
||||||
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
|
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
|
||||||
<li>
|
<li>
|
||||||
<p>AI improvements for <code>as.mo</code>:</p>
|
<p>AI improvements for <code>as.mo</code>:</p>
|
||||||
@ -1826,13 +1825,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R">
|
<code class="sourceCode R">
|
||||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||||
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||||
<p>For lists, subsetting is possible:</p>
|
<p>For lists, subsetting is possible:</p>
|
||||||
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
|
<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
|
||||||
<code class="sourceCode R">
|
<code class="sourceCode R">
|
||||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
</div>
|
</div>
|
||||||
@ -1906,13 +1905,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
|||||||
<ul>
|
<ul>
|
||||||
<li>A vignette to explain its usage</li>
|
<li>A vignette to explain its usage</li>
|
||||||
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
|
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
|
||||||
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
|
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
|
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
|
||||||
</li>
|
</li>
|
||||||
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
|
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
|
||||||
</li>
|
</li>
|
||||||
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
||||||
</li>
|
</li>
|
||||||
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
|
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
|
||||||
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
|
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
|
||||||
|
|||||||
@ -12,7 +12,7 @@ articles:
|
|||||||
datasets: datasets.html
|
datasets: datasets.html
|
||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
welcome_to_AMR: welcome_to_AMR.html
|
welcome_to_AMR: welcome_to_AMR.html
|
||||||
last_built: 2021-02-18T22:21Z
|
last_built: 2021-02-09T11:26Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.github.io/AMR//reference
|
reference: https://msberends.github.io/AMR//reference
|
||||||
article: https://msberends.github.io/AMR//articles
|
article: https://msberends.github.io/AMR//articles
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -83,7 +83,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
@ -318,7 +318,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
|||||||
<span class='co'># See ?example_isolates.</span>
|
<span class='co'># See ?example_isolates.</span>
|
||||||
|
|
||||||
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
|
<span class='co'># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span>
|
||||||
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>]</span>
|
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
|
||||||
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
|
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
|
||||||
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mo"</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
|
<span class='va'>example_isolates</span><span class='op'>[</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mo"</span>, <span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>]</span>
|
||||||
|
|
||||||
|
|||||||
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -82,7 +82,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9019</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -81,7 +81,7 @@
|
|||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9020</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9018</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|||||||
@ -123,8 +123,10 @@ echo
|
|||||||
echo "••••••••••••••••••••"
|
echo "••••••••••••••••••••"
|
||||||
echo "• Building package •"
|
echo "• Building package •"
|
||||||
echo "••••••••••••••••••••"
|
echo "••••••••••••••••••••"
|
||||||
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
|
echo "• Removing old build from 'data-raw/'..."
|
||||||
Rscript -e "x <- devtools::build(path = 'data-raw/AMR_latest.tar.gz', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
|
rm data-raw/AMR_*.tar.gz
|
||||||
|
echo "• Building 'data-raw/AMR_${new_version}.tar.gz'..."
|
||||||
|
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
|
||||||
echo "• Installing..."
|
echo "• Installing..."
|
||||||
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
||||||
echo
|
echo
|
||||||
|
|||||||
4
index.md
4
index.md
@ -125,12 +125,10 @@ It will be downloaded and installed automatically. For RStudio, click on the men
|
|||||||
The latest and unpublished development version can be installed from GitHub using:
|
The latest and unpublished development version can be installed from GitHub using:
|
||||||
|
|
||||||
```r
|
```r
|
||||||
install.packages("remotes") # if you haven't already
|
install.packages("remotes")
|
||||||
remotes::install_github("msberends/AMR")
|
remotes::install_github("msberends/AMR")
|
||||||
```
|
```
|
||||||
|
|
||||||
You can also download the latest build from our repository: <https://github.com/msberends/AMR/raw/master/data-raw/AMR_latest.tar.gz>
|
|
||||||
|
|
||||||
### Get started
|
### Get started
|
||||||
|
|
||||||
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
|
To find out how to conduct AMR data analysis, please [continue reading here to get started](./articles/AMR.html) or click the links in the 'How to' menu.
|
||||||
|
|||||||
@ -85,7 +85,7 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
|
|||||||
# See ?example_isolates.
|
# See ?example_isolates.
|
||||||
|
|
||||||
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||||
example_isolates[, carbapenems()]
|
example_isolates[, c(carbapenems())]
|
||||||
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
||||||
example_isolates[, c("mo", aminoglycosides())]
|
example_isolates[, c("mo", aminoglycosides())]
|
||||||
|
|
||||||
|
|||||||
@ -88,7 +88,7 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
|
|||||||
/* adjusted colour for all real links; having href attribute */
|
/* adjusted colour for all real links; having href attribute */
|
||||||
color: #128f76;
|
color: #128f76;
|
||||||
}
|
}
|
||||||
.ot, .dv, .fl, .cn {
|
.ot, .dv {
|
||||||
/* numbers and TRUE/FALSE */
|
/* numbers and TRUE/FALSE */
|
||||||
color: slategray;
|
color: slategray;
|
||||||
}
|
}
|
||||||
@ -187,13 +187,10 @@ div[id^=last-updated] h2 {
|
|||||||
}
|
}
|
||||||
|
|
||||||
/* tables, make them look like scientific ones */
|
/* tables, make them look like scientific ones */
|
||||||
table {
|
.table {
|
||||||
font-size: 90%;
|
font-size: 90%;
|
||||||
}
|
}
|
||||||
table * {
|
.table td {
|
||||||
vertical-align: middle !important;
|
|
||||||
}
|
|
||||||
table td {
|
|
||||||
padding: 4px !important;
|
padding: 4px !important;
|
||||||
}
|
}
|
||||||
thead {
|
thead {
|
||||||
|
|||||||
@ -84,9 +84,6 @@ test_that("mo_property works", {
|
|||||||
expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
|
expect_output(print(mo_gramstain("Escherichia coli", language = "fr")))
|
||||||
|
|
||||||
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
|
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
|
||||||
|
|
||||||
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
|
|
||||||
expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
|
|
||||||
|
|
||||||
# manual property function
|
# manual property function
|
||||||
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
|
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user