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(v3.0.1.9082) website
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Package: AMR
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Version: 3.0.1.9081
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Date: 2026-06-27
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Version: 3.0.1.9082
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Date: 2026-07-03
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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2
NEWS.md
2
NEWS.md
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# AMR 3.0.1.9081
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# AMR 3.0.1.9082
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Planned as v3.1.0, end of June 2026.
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@@ -22,7 +22,7 @@ Please visit our comprehensive package website <https://amr-for-r.org> to read m
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Overview:
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* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
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* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
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* **Peer-reviewed**, used in over 175 countries, cited over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
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* Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
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* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
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* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
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@@ -10,8 +10,8 @@ Overview:
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- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
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data analysis in a One Health approach
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- **Peer-reviewed**, used in over 175 countries, available in 28
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languages
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- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
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available in 28 languages
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- Generates **antibiograms** - WISCA for empiric coverage estimates, or
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traditional/syndromic for AMR surveillance
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- Provides the **full microbiological taxonomy** of ~97 000 distinct
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@@ -20,7 +20,7 @@ AMR:::reset_all_thrown_messages()
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# The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
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* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
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* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
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* **Peer-reviewed**, used in over 175 countries, cites over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
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* Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
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* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
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* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
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With the help of contributors from all corners of the world, the `AMR` package is available in `r lang_txt`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
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The `AMR` package was cited [over 100 times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC) in scientific research.
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## Practical examples
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### Filtering and selecting data
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21
index.md
21
index.md
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- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
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data analysis in a One Health approach
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- **Peer-reviewed**, used in over 175 countries, available in 28
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languages
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- **Peer-reviewed**, used in over 175 countries, cites over 100 times,
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available in 28 languages
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- Generates **antibiograms** - WISCA for empiric coverage estimates, or
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traditional/syndromic for AMR surveillance
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- Provides the **full microbiological taxonomy** of ~97 000 distinct
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@@ -144,6 +144,10 @@ Urdu, and
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Vietnamese. Antimicrobial drug (group) names and colloquial
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microorganism names are provided in these languages.
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The `AMR` package was cited [over 100
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times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
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in scientific research.
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## Practical examples
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### Filtering and selecting data
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@@ -229,7 +233,7 @@ wisca(example_isolates,
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| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
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|:------------------------|:-------------------------------------|:-------------------------------------|
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| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) |
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| 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
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WISCA supports stratification by any clinical variable, so you can
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generate syndrome-specific or ward-specific coverage estimates:
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| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
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|:----------------|:------------------------|:-------------------------------------|:-------------------------------------|
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| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) |
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| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) |
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| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) |
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| Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
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| ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
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| Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
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**For AMR surveillance**, traditional antibiograms remain the right tool
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for tracking resistance per species over time:
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@@ -349,11 +353,6 @@ example_isolates %>%
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summarise(across(c(GEN, TOB),
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list(total_R = resistance,
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conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
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#> ℹ `resistance()` assumes the EUCAST guideline and thus
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#> considers the 'I' category susceptible. Set the `guideline`
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#> argument or the `AMR_guideline` option to either "CLSI" or
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#> "EUCAST", see `?AMR-options`.
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#> ℹ This message will be shown once per session.
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#> # A tibble: 3 × 5
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#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
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#> <chr> <dbl> <chr> <dbl> <chr>
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