From 374627273f46e2f35a3a52258c9a97dd1396a4b3 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 10 Jun 2024 08:40:19 +0000 Subject: [PATCH] cli-147-2111 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 30 +-- articles/EUCAST.html | 2 +- articles/MDR.html | 2 +- articles/PCA.html | 2 +- articles/WHONET.html | 2 +- articles/datasets.html | 18 +- articles/index.html | 2 +- articles/other_pkg.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- endorsement_clsi_eucast.jpg | Bin 0 -> 99248 bytes index.html | 11 +- news/index.html | 24 +- pkgdown.yml | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/Rplot010.png | Bin 9232 -> 8807 bytes reference/Rplot011.png | Bin 15608 -> 13350 bytes 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_groups.html | 2 +- reference/antibiogram.html | 2 +- reference/antibiotic_class_selectors.html | 18 +- reference/antibiotics.html | 12 +- reference/as.ab.html | 2 +- reference/as.av.html | 2 +- reference/as.disk.html | 22 +- reference/as.mic.html | 9 +- reference/as.mo.html | 2 +- reference/as.sir.html | 258 ++++++++++++---------- 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 | 10 +- reference/dosage.html | 2 +- reference/eucast_rules.html | 2 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/export_ncbi_biosample.html | 211 ++++++++++++++++++ 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 | 15 +- 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-1.png | Bin 26360 -> 26418 bytes reference/plot-10.png | Bin 27064 -> 26183 bytes reference/plot-11.png | Bin 41789 -> 37985 bytes reference/plot-4.png | Bin 40277 -> 40304 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 2 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 2 +- reference/translate.html | 2 +- search.json | 2 +- sitemap.xml | 3 + 85 files changed, 540 insertions(+), 251 deletions(-) create mode 100644 endorsement_clsi_eucast.jpg create mode 100644 reference/export_ncbi_biosample.html diff --git a/404.html b/404.html index 76f2c731..2fbdc2f7 100644 --- a/404.html +++ b/404.html @@ -37,7 +37,7 @@ AMR (for R) - 2.1.1.9037 + 2.1.1.9043 + + + + + +
+
+
+ +
+

Export Data Set as NCBI BioSample Antibiogram

+
+ +
+

Usage

+
export_ncbi_biosample(
+  x,
+  filename = paste0("biosample_", format(Sys.time(), "%Y-%m-%d-%H%M%S"), ".xlsx"),
+  type = "pathogen MIC",
+  columns = where(is.mic),
+  save_as_xlsx = TRUE
+)
+
+ +
+

Arguments

+
x
+

a data set

+ + +
filename
+

a character string specifying the file name

+ + +
type
+

a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see https://www.ncbi.nlm.nih.gov/biosample/docs/

+ +
+ +
+ + +
+ + + + + + + diff --git a/reference/first_isolate.html b/reference/first_isolate.html index 281ffe48..954e8bcf 100644 --- a/reference/first_isolate.html +++ b/reference/first_isolate.html @@ -12,7 +12,7 @@ AMR (for R) - 2.1.1.9037 + 2.1.1.9043