Introduction
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:
-| 2026-06-27 |
+2026-07-03 |
abcd |
Escherichia coli |
S |
S |
-| 2026-06-27 |
+2026-07-03 |
abcd |
Escherichia coli |
S |
R |
-| 2026-06-27 |
+2026-07-03 |
efgh |
Escherichia coli |
R |
diff --git a/articles/AMR.md b/articles/AMR.md
index 711f14054..0e248aea6 100644
--- a/articles/AMR.md
+++ b/articles/AMR.md
@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 27 June 2026.
+methodology remains unchanged. This page was generated on 03 July 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-06-27 | abcd | Escherichia coli | S | S |
-| 2026-06-27 | abcd | Escherichia coli | S | R |
-| 2026-06-27 | efgh | Escherichia coli | R | S |
+| 2026-07-03 | abcd | Escherichia coli | S | S |
+| 2026-07-03 | abcd | Escherichia coli | S | R |
+| 2026-07-03 | efgh | Escherichia coli | R | S |
### Needed R packages
diff --git a/articles/AMR_for_Python.html b/articles/AMR_for_Python.html
index a6334f880..6a0b0bdfc 100644
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -30,7 +30,7 @@
AMR (for R)
- 3.0.1.9081
+ 3.0.1.9082
-| 70% (64.7-75.2%) |
-93.6% (92.2-95.1%) |
-89.8% (87-92.5%) |
+69.9% (64.9-75.3%) |
+93.6% (92.1-95%) |
+89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:
@@ -219,21 +220,21 @@
| Clinical |
-74.6% (68.6-80.6%) |
-93.7% (92.1-95.1%) |
-90.4% (87-93.1%) |
+74.5% (68.6-80.5%) |
+93.7% (91.7-95.1%) |
+90.4% (87.1-93.1%) |
| ICU |
-57% (48.6-65.7%) |
-86.8% (83.6-89.8%) |
-82.9% (78.1-87.3%) |
+57% (48.6-65.6%) |
+86.7% (83.3-89.9%) |
+83% (78.1-87.5%) |
| Outpatient |
-56.9% (45.9-68.2%) |
-76.7% (70.6-82.3%) |
-68% (57.6-77.2%) |
+57.4% (46-69.1%) |
+76.7% (70.5-82.7%) |
+67.7% (57.3-77.4%) |
@@ -391,11 +392,6 @@
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-
#> ℹ `resistance()` assumes the EUCAST guideline and thus
-
#> considers the 'I' category susceptible. Set the `guideline`
-
#> argument or the `AMR_guideline` option to either "CLSI" or
-
#> "EUCAST", see `?AMR-options`.
-
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr>
diff --git a/index.md b/index.md
index 00b7953f0..ef163eaff 100644
--- a/index.md
+++ b/index.md
@@ -2,8 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
- languages
+- **Peer-reviewed**, used in over 175 countries, cites over 100 times,
+ available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -89,6 +89,10 @@ Swahili,  Swedish,  Turkish,
Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.
+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.
+
## Practical examples
### Filtering and selecting data
@@ -183,7 +187,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
-| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) |
+| 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -199,9 +203,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
-| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) |
-| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) |
-| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) |
+| Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
+| ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
+| Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
@@ -310,11 +314,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-#> ℹ `resistance()` assumes the EUCAST guideline and thus
-#> considers the 'I' category susceptible. Set the `guideline`
-#> argument or the `AMR_guideline` option to either "CLSI" or
-#> "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#>
diff --git a/llms.txt b/llms.txt
index 1b703546a..fa9958d46 100644
--- a/llms.txt
+++ b/llms.txt
@@ -2,8 +2,8 @@
- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
- languages
+- **Peer-reviewed**, used in over 175 countries, cites over 100 times,
+ available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -89,6 +89,10 @@ Swahili,  Swedish,  Turkish,
Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.
+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.
+
## Practical examples
### Filtering and selecting data
@@ -183,7 +187,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|
-| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) |
+| 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates:
@@ -199,9 +203,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:---|:---|:---|:---|
-| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) |
-| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) |
-| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) |
+| Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
+| ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
+| Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
**For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time:
@@ -310,11 +314,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-#> ℹ `resistance()` assumes the EUCAST guideline and thus
-#> considers the 'I' category susceptible. Set the `guideline`
-#> argument or the `AMR_guideline` option to either "CLSI" or
-#> "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#>
diff --git a/news/index.html b/news/index.html
index 195969010..797852ed1 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
AMR (for R)
- 3.0.1.9081
+ 3.0.1.9082