From 33e262ed9b648e6da28d19ecd2f569335d301fbb Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 11 Mar 2026 15:20:20 +0000 Subject: [PATCH] Built site for AMR@3.0.1.9034: 4dc3ec0 --- 404.html | 2 +- CLAUDE.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 10 +- articles/AMR.md | 8 +- articles/AMR_for_Python.html | 2 +- articles/AMR_with_tidymodels.html | 2 +- articles/EUCAST.html | 2 +- articles/PCA.html | 2 +- articles/WHONET.html | 2 +- articles/WISCA.html | 2 +- articles/datasets.html | 4 +- articles/index.html | 2 +- authors.html | 2 +- index.html | 2 +- llms.txt | 9 +- news/index.html | 16 +-- news/index.md | 15 ++- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/WHOCC.html | 2 +- reference/WHONET.html | 2 +- reference/ab_from_text.html | 2 +- reference/ab_property.html | 2 +- reference/add_custom_antimicrobials.html | 2 +- reference/add_custom_microorganisms.html | 2 +- reference/age.html | 22 ++--- reference/age.md | 20 ++-- reference/age_groups.html | 2 +- reference/amr-tidymodels.html | 2 +- reference/amr_course.html | 119 +++++++++++++++++++++++ reference/amr_course.md | 58 +++++++++++ reference/antibiogram.html | 2 +- reference/antimicrobial_selectors.html | 2 +- reference/antimicrobials.html | 2 +- reference/as.ab.html | 2 +- reference/as.av.html | 2 +- reference/as.disk.html | 2 +- reference/as.mic.html | 2 +- reference/as.mo.html | 2 +- reference/as.sir.html | 10 +- reference/as.sir.md | 8 +- reference/atc_online.html | 2 +- reference/av_from_text.html | 2 +- reference/av_property.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 2 +- reference/clinical_breakpoints.html | 2 +- reference/count.html | 2 +- reference/custom_eucast_rules.html | 2 +- reference/custom_mdro_guideline.html | 2 +- reference/dosage.html | 2 +- reference/esbl_isolates.html | 2 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/export_ncbi_biosample.html | 2 +- reference/first_isolate.html | 2 +- reference/g.test.html | 2 +- reference/get_episode.html | 2 +- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 11 ++- reference/index.md | 9 +- reference/interpretive_rules.html | 14 +-- reference/interpretive_rules.md | 7 -- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 2 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 2 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 2 +- reference/microorganisms.codes.html | 2 +- reference/microorganisms.groups.html | 2 +- reference/microorganisms.html | 2 +- reference/mo_matching_score.html | 2 +- reference/mo_property.html | 2 +- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 2 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 2 +- reference/top_n_microorganisms.html | 2 +- reference/translate.html | 2 +- search.json | 2 +- sitemap.xml | 1 + 92 files changed, 337 insertions(+), 154 deletions(-) create mode 100644 reference/amr_course.html create mode 100644 reference/amr_course.md diff --git a/404.html b/404.html index ca775d2cd..a1a742627 100644 --- a/404.html +++ b/404.html @@ -31,7 +31,7 @@ AMR (for R) - 3.0.1.9033 + 3.0.1.9034 + + + + + +
+
+
+

Download and Unpack an AMR Course Repository

+ Source: R/amr_course.R +
amr_course.Rd
+
+ +
+

Downloads and unpacks a GitHub repository containing course materials, using usethis::use_course(). This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.

+
+ +
+

Usage

+ 
amr_course(github_repo, branch = "main", ...)
+
+ +
+

Arguments

+ + +
github_repo
+

A character string specifying the GitHub repository with username and repo name, e.g. "https://github.com/username/repo".

+ + +
branch
+

A character string specifying the branch to download. Defaults to "main".

+ + +
...
+

Additional arguments passed on to usethis::use_course().

+ +
+
+

Value

+

Called for its side effect. usethis::use_course() will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever usethis::use_course() returns.

+
+
+

Details

+

This function constructs a ZIP archive URL from the provided github_repo and branch, then delegates to usethis::use_course() to handle the download and extraction.

+

The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.

+
+
+

See also

+

usethis::use_course()

+
+ +
+

Examples

+ 
if (FALSE) { # \dontrun{
+
+# Let this run by users, e.g., webinar participants
+amr_course("https://github.com/my_user_name/our_AMR_course")
+} # }
+
+
+
+ + +
+ + + + + + + diff --git a/reference/amr_course.md b/reference/amr_course.md new file mode 100644 index 000000000..34282e5ea --- /dev/null +++ b/reference/amr_course.md @@ -0,0 +1,58 @@ +# Download and Unpack an AMR Course Repository + +Downloads and unpacks a GitHub repository containing course materials, +using `usethis::use_course()`. This is a convenience wrapper intended +for use in educational settings, such as workshops or tutorials +associated with the AMR package. + +## Usage + +``` r +amr_course(github_repo, branch = "main", ...) +``` + +## Arguments + +- github_repo: + + A character string specifying the GitHub repository with username and + repo name, e.g. `"https://github.com/username/repo"`. + +- branch: + + A character string specifying the branch to download. Defaults to + `"main"`. + +- ...: + + Additional arguments passed on to `usethis::use_course()`. + +## Value + +Called for its side effect. `usethis::use_course()` will prompt the user +to choose a destination and open the extracted project. Returns +invisibly whatever `usethis::use_course()` returns. + +## Details + +This function constructs a ZIP archive URL from the provided +`github_repo` and `branch`, then delegates to `usethis::use_course()` to +handle the download and extraction. + +The function is designed for interactive use in course or workshop +settings and is not intended for use in non-interactive or automated +pipelines. + +## See also + +`usethis::use_course()` + +## Examples + +``` r +if (FALSE) { # \dontrun{ + +# Let this run by users, e.g., webinar participants +amr_course("https://github.com/my_user_name/our_AMR_course") +} # } +``` diff --git a/reference/antibiogram.html b/reference/antibiogram.html index 8f95544fa..e99efe537 100644 --- a/reference/antibiogram.html +++ b/reference/antibiogram.html @@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye AMR (for R) - 3.0.1.9033 + 3.0.1.9034