From 7f1c20a0e8c033aa1321839eb77fd8b4941aac93 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 11 Mar 2023 13:32:27 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9148@262598b --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 267 +++++++++--------- .../figure-html/unnamed-chunk-13-1.png | Bin 42740 -> 42899 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 56 ++-- articles/PCA.html | 2 +- articles/SPSS.html | 6 +- articles/WHONET.html | 2 +- articles/datasets.html | 4 +- articles/index.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 2 +- news/index.html | 26 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/Rplot005.png | Bin 13182 -> 13249 bytes reference/Rplot006.png | Bin 13199 -> 13227 bytes reference/Rplot007.png | Bin 13063 -> 13438 bytes reference/Rplot008.png | Bin 18932 -> 18108 bytes reference/Rplot009.png | Bin 8638 -> 8579 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 | 37 +-- reference/antibiotic_class_selectors.html | 2 +- reference/antibiotics.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 | 22 +- 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/dosage.html | 2 +- reference/eucast_rules.html | 2 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/first_isolate.html | 2 +- reference/g.test.html | 2 +- reference/get_episode.html | 110 ++++---- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 2 +- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 2 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 6 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 73 ++--- reference/microorganisms.codes.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 26657 -> 26913 bytes reference/plot-2.png | Bin 26495 -> 27615 bytes reference/plot-3.png | Bin 27943 -> 27972 bytes reference/plot-4.png | Bin 39519 -> 39727 bytes reference/plot-5.png | Bin 39090 -> 39742 bytes reference/plot-6.png | Bin 38235 -> 38976 bytes reference/plot-7.png | Bin 37582 -> 37837 bytes reference/plot-8.png | Bin 56465 -> 54976 bytes reference/plot-9.png | Bin 26378 -> 26304 bytes reference/plot.html | 26 +- reference/proportion.html | 2 +- reference/random.html | 34 +-- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 91 files changed, 414 insertions(+), 403 deletions(-) diff --git a/404.html b/404.html index 9cfc0b9f..2817ea22 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9147 + 1.8.2.9148
+generated on 11 March 2023.
# method 1, be explicit about the columns:
-our_data <- our_data %>%
+our_data <- our_data %>%
mutate_at(vars(AMX:GEN), as.sir)
# method 2, let the AMR package determine the eligible columns
-our_data <- our_data %>%
+our_data <- our_data %>%
mutate_if(is_sir_eligible, as.sir)
# result:
@@ -592,7 +592,7 @@ impression, as it comes with support for the new mo
and
frequency table with count()
based on the name of the
microorganisms:
-our_data %>%
+our_data %>%
count(mo_name(bacteria), sort = TRUE)
#> # A tibble: 4 × 2
#> `mo_name(bacteria)` n
@@ -602,7 +602,7 @@ microorganisms:
#> 3 Streptococcus pneumoniae 426
#> 4 Klebsiella pneumoniae 326
-our_data_1st %>%
+our_data_1st %>%
count(mo_name(bacteria), sort = TRUE)
#> # A tibble: 4 × 2
#> `mo_name(bacteria)` n
@@ -788,7 +788,8 @@ antibiograms:
antibiogram(our_data_1st,
- ab_transform = "name")
+ ab_transform = "name"
+)
@@ -841,8 +842,9 @@ antibiograms:
antibiogram(our_data_1st,
- ab_transform = "name",
- language = "es") # support for 20 languages
+ ab_transform = "name",
+ language = "es"
+) # support for 20 languages
Pathogen (N min-max) | @@ -938,12 +941,14 @@ antibiograms:
---|
Syndromic Group | @@ -957,119 +962,120 @@ antibiograms:|||||||||
---|---|---|---|---|---|---|---|---|---|
Cardial | -E. coli (431-431) | -63 | -54 | -57 | -63 | +E. coli (401-401) +67 | +61 | +59 | +65 |
Respiratory | -E. coli (396-396) | -64 | -61 | -58 | -63 | +E. coli (403-403) +60 | +55 | +54 | +59 |
Rheumatic | -E. coli (423-423) | +E. coli (446-446)65 | +59 | 60 | -58 | -63 | +64 | ||
Cardial | -K. pneumoniae (105-105) | -63 | -54 | -59 | +K. pneumoniae (99-99) +65 | 61 | +60 | +59 | |
Respiratory | K. pneumoniae (110-110) | +62 | +49 | +56 | 60 | -54 | -55 | -63 | |
Rheumatic | -K. pneumoniae (101-101) | -66 | -50 | +K. pneumoniae (107-107) +63 | +49 | +61 | +62 | +||
Cardial | ++S. aureus (235-235) | +64 | +55 | +61 | +57 | +||||
Respiratory | ++S. aureus (208-208) | +62 | +61 | +57 | +65 | +||||
Rheumatic | ++S. aureus (218-218) | +67 | +55 | +53 | +67 | +||||
Cardial | ++S. pneumoniae (132-132) | 62 | 56 | +62 | +68 | ||||
Cardial | --S. aureus (225-225) | -66 | -57 | -53 | -61 | -||||
Respiratory | -S. aureus (217-217) | +S. pneumoniae (137-137)60 | -55 | +54 | +61 | 61 | -64 | -||
Rheumatic | --S. aureus (219-219) | -67 | -58 | -58 | -64 | -||||
Cardial | --S. pneumoniae (152-152) | -67 | -57 | -64 | -63 | -||||
Respiratory | --S. pneumoniae (122-122) | -67 | -57 | -64 | -67 | ||||
Rheumatic | -S. pneumoniae (125-125) | -57 | -53 | -50 | -67 | +S. pneumoniae (130-130) +70 | +58 | +56 | +68 |
antibiogram(our_data_1st,
- # you can use AB selectors here as well:
- antibiotics = c(penicillins(), aminoglycosides()),
- syndromic_group = "condition",
- mo_transform = "gramstain")
+ # you can use AB selectors here as well:
+ antibiotics = c(penicillins(), aminoglycosides()),
+ syndromic_group = "condition",
+ mo_transform = "gramstain"
+)
#> ℹ For penicillins() using columns 'AMX' (amoxicillin) and 'AMC'
#> (amoxicillin/clavulanic acid)
#> ℹ For aminoglycosides() using column 'GEN' (gentamicin)
-# WISCA:
+# WISCA:
# (we lack some details, but it could contain a filter on e.g. >65 year-old males)
wisca <- antibiogram(our_data_1st,
- antibiotics = c("AMC", "AMC+CIP", "AMC+GEN"),
- syndromic_group = "condition",
- mo_transform = "gramstain")
+ antibiotics = c("AMC", "AMC+CIP", "AMC+GEN"),
+ syndromic_group = "condition",
+ mo_transform = "gramstain"
+)
wisca
Cardial | -Gram-negative (536-536) | -63 | -75 | -75 | +Gram-negative (500-500) | +66 | +77 | +77 |
Respiratory | -Gram-negative (506-506) | -63 | -77 | -75 | +Gram-negative (513-513) | +60 | +72 | +71 |
Rheumatic | -Gram-negative (524-524) | +Gram-negative (553-553) | 65 | +78 | 76 | -75 | ||
Cardial | -Gram-positive (377-377) | -67 | -78 | +Gram-positive (367-367) | +63 | +79 | 75 | |
Respiratory | -Gram-positive (339-339) | -63 | -77 | +Gram-positive (345-345) | +61 | 76 | +73 | |
Rheumatic | -Gram-positive (344-344) | -63 | +Gram-positive (348-348) | +68 | 77 | -76 | +79 |
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