vignettes/AMR.Rmd
AMR.Rmd
So only 53% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the @@ -634,7 +634,7 @@ it with the data_1st <- data %>% filter_first_isolate() # Including isolates from ICU. -
filter()
data_1st <- data %>% filter_first_isolate() # Including isolates from ICU.
So we end up with 10,602 isolates for analysis. Now our data looks +
So we end up with 10,609 isolates for analysis. Now our data looks like:
head(data_1st)
Time for the analysis!
data_1st %>% freq(genus, species)
Frequency table
Class: character -Length: 10,602 -Available: 10,602 (100%, NA: 0 = 0%) +Length: 10,609 +Available: 10,609 (100%, NA: 0 = 0%) Unique: 4
Shortest: 16 Longest: 24
If you want to get a quick glance of the number of isolates in @@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
proportion_SI()
data_1st %>% resistance(AMX) -# [1] 0.5470666
Or can be used in conjunction with group_by() and summarise(), both from the dplyr package:
group_by()
summarise()
dplyr
@@ -1152,19 +1152,19 @@ own: Hospital A -0.5567929 +0.5376442 Hospital B -0.5470541 +0.5473011 Hospital C -0.5369212 +0.5522855 Hospital D -0.5402844 +0.5400188 @@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital A -0.5567929 -3143 +0.5376442 +3294 Hospital B -0.5470541 -3751 +0.5473011 +3594 Hospital C -0.5369212 -1598 +0.5522855 +1597 Hospital D -0.5402844 -2110 +0.5400188 +2124 @@ -1230,27 +1230,27 @@ therapies very easily: Escherichia -0.7682533 -0.8729270 -0.9763084 +0.7688160 +0.8714686 +0.9775717 Klebsiella -0.8004946 -0.8961253 -0.9777411 +0.8177128 +0.8950989 +0.9819433 Staphylococcus -0.7955390 -0.8892193 -0.9795539 +0.8033687 +0.8919810 +0.9794947 Streptococcus -0.5330739 +0.5413859 0.0000000 -0.5330739 +0.5413859 @@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as Hospital A -55.7% -26.3% +53.8% +26.2% Hospital B 54.7% -27.3% +26.7% Hospital C -53.7% -26.7% +55.2% +25.7% Hospital D 54.0% -26.0% +25.4% @@ -1410,18 +1410,18 @@ classes) <mic> and <disk>: mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 4 >=256 0.25 <=0.001 1 0.002 8 0.025 8 -# [10] 1 64 0.0625 0.025 16 0.002 1 8 0.01 -# [19] 0.025 0.01 4 <=0.001 >=256 0.25 0.125 32 4 -# [28] 64 <=0.001 64 <=0.001 8 4 4 0.0625 0.125 -# [37] 0.25 4 32 0.5 64 0.002 0.25 0.5 1 -# [46] 4 0.005 1 32 0.005 0.005 0.125 16 0.025 -# [55] 32 0.5 32 0.002 8 64 0.5 0.025 2 -# [64] 32 0.5 4 0.0625 0.002 0.002 0.01 0.005 2 -# [73] 4 0.002 0.5 64 0.125 32 0.01 4 <=0.001 -# [82] 0.025 1 <=0.001 0.25 0.0625 0.002 4 8 0.5 -# [91] 0.25 128 32 0.025 0.125 32 32 32 0.5 -# [100] 0.002
<mic>
<disk>
mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 4 >=256 0.25 <=0.001 1 0.002 8 0.025 8 -# [10] 1 64 0.0625 0.025 16 0.002 1 8 0.01 -# [19] 0.025 0.01 4 <=0.001 >=256 0.25 0.125 32 4 -# [28] 64 <=0.001 64 <=0.001 8 4 4 0.0625 0.125 -# [37] 0.25 4 32 0.5 64 0.002 0.25 0.5 1 -# [46] 4 0.005 1 32 0.005 0.005 0.125 16 0.025 -# [55] 32 0.5 32 0.002 8 64 0.5 0.025 2 -# [64] 32 0.5 4 0.0625 0.002 0.002 0.01 0.005 2 -# [73] 4 0.002 0.5 64 0.125 32 0.01 4 <=0.001 -# [82] 0.025 1 <=0.001 0.25 0.0625 0.002 4 8 0.5 -# [91] 0.25 128 32 0.025 0.125 32 32 32 0.5 -# [100] 0.002
# base R: plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro") disk_values # Class 'disk' -# [1] 24 24 29 30 27 19 20 20 20 19 24 26 19 21 24 28 30 25 25 22 30 29 18 30 18 -# [26] 25 21 23 31 30 26 17 23 21 27 27 24 28 25 22 18 25 29 25 30 30 23 30 23 26 -# [51] 26 20 31 20 18 27 26 22 22 20 30 23 20 26 22 31 21 22 23 25 24 23 23 18 18 -# [76] 17 19 25 17 27 25 17 26 21 24 30 31 30 18 19 30 23 17 27 30 18 21 26 28 24
# base R: plot(disk_values, mo = "E. coli", ab = "cipro")
head(my_TB_data) # rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -# 1 R R S S S R -# 2 S I I R R R -# 3 R I S S S R -# 4 I R S R I I -# 5 S R R R R I -# 6 R I S R I R +# 1 S S I R R S +# 2 I R I S S R +# 3 S I R S S S +# 4 R S R I I R +# 5 I I R I S I +# 6 S I I S S S # kanamycin -# 1 R -# 2 R -# 3 I -# 4 S +# 1 I +# 2 I +# 3 R +# 4 I # 5 S # 6 I
We can now add the interpretation of MDR-TB to our data set. You can @@ -428,40 +428,40 @@ Unique: 5
vignettes/SPSS.Rmd
SPSS.Rmd
ggplot_rsi() diff --git a/articles/datasets.html b/articles/datasets.html index b1ff1d9a..5b49c797 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -166,7 +166,7 @@ Data sets for download / own use - 10 December 2022 + 11 December 2022 Source: vignettes/datasets.Rmd datasets.Rmd @@ -2003,12 +2003,12 @@ reality and can be used to practise AMR data analysis. diff --git a/articles/index.html b/articles/index.html index 3724c4f5..2a7901d0 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -157,11 +157,11 @@ diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index 5365652c..51617ab9 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -350,12 +350,12 @@ model might be more appropriate: diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 98631857..3df93e90 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -272,12 +272,12 @@ included with the package. diff --git a/authors.html b/authors.html index ca367af3..70cbe86f 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -240,11 +240,11 @@ diff --git a/index.html b/index.html index be3e753e..bbfe5b80 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -547,9 +547,9 @@ Partners -The development of this package is part of, related to, or made possible by: +The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives: - + @@ -612,12 +612,12 @@ diff --git a/logo_certe.png b/logo_certe.png deleted file mode 100755 index 001925f1..00000000 Binary files a/logo_certe.png and /dev/null differ diff --git a/logo_certe.svg b/logo_certe.svg new file mode 100644 index 00000000..0466bd3b --- /dev/null +++ b/logo_certe.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/logo_umcg.png b/logo_umcg.png deleted file mode 100755 index d562a34e..00000000 Binary files a/logo_umcg.png and /dev/null differ diff --git a/logo_umcg.svg b/logo_umcg.svg new file mode 100644 index 00000000..dda994e7 --- /dev/null +++ b/logo_umcg.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/news/index.html b/news/index.html index cae00c52..bcc42339 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -132,10 +132,10 @@ -AMR 1.8.2.9060 +AMR 1.8.2.9061 This version will eventually become v2.0! We’re happy to reach a new major milestone soon! -Breaking +Breaking Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons: CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them @@ -152,7 +152,7 @@ Using units in ab_ddd(..., units = "...") had been deprecated and is now not supported anymore. Use ab_ddd_units() instead. -New +New EUCAST 2022 and CLSI 2022 guidelines have been added for as.rsi(). EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for eucast_rules() to apply EUCAST Expert Rules. Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The AMR package is now available in 16 languages. The automatic language determination will give a note on systems in supported languages. @@ -194,7 +194,7 @@ -Changes +Changes For as.rsi(): Fixed certain EUCAST breakpoints for MIC values Allow NA values (e.g. as.rsi(as.disk(NA), ...)) @@ -233,7 +233,7 @@ Cleaning columns with as.rsi(), as.mic(), or as.disk() will now show the column name in the warning for invalid results -Other +Other New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input All R and Rmd files in this project are now styled using the styler package @@ -377,11 +377,11 @@ diff --git a/pkgdown.yml b/pkgdown.yml index 3a419793..7aa08cbc 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -11,7 +11,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2022-12-10T09:13Z +last_built: 2022-12-11T10:47Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html index 5c308261..3341c10d 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -142,11 +142,11 @@ diff --git a/reference/AMR.html b/reference/AMR.html index 66d3b537..aaaf9808 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -62,7 +62,7 @@ Principal component analysis for AMR AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -274,11 +274,11 @@ Principal component analysis for AMR diff --git a/reference/Rplot005.png b/reference/Rplot005.png index b05aa84b..add54c5e 100644 Binary files a/reference/Rplot005.png and b/reference/Rplot005.png differ diff --git a/reference/Rplot006.png b/reference/Rplot006.png index 37d56121..b85b5f6a 100644 Binary files a/reference/Rplot006.png and b/reference/Rplot006.png differ diff --git a/reference/Rplot007.png b/reference/Rplot007.png index 13a009f8..ba06d14e 100644 Binary files a/reference/Rplot007.png and b/reference/Rplot007.png differ diff --git a/reference/Rplot008.png b/reference/Rplot008.png index bfd89427..b22ea655 100644 Binary files a/reference/Rplot008.png and b/reference/Rplot008.png differ diff --git a/reference/Rplot009.png b/reference/Rplot009.png index e2832891..90263ca0 100644 Binary files a/reference/Rplot009.png and b/reference/Rplot009.png differ diff --git a/reference/WHOCC.html b/reference/WHOCC.html index 8c9e09ca..e7b2e7df 100644 --- a/reference/WHOCC.html +++ b/reference/WHOCC.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -141,8 +141,7 @@ WHOCC - -This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). +This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). These have become the gold standard for international drug utilisation monitoring and research. The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest. NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/. @@ -168,11 +167,11 @@ This package contains all ~550 antibiotic, antimycotic and antiviral dru diff --git a/reference/WHONET.html b/reference/WHONET.html index 85a2311a..c3759c91 100644 --- a/reference/WHONET.html +++ b/reference/WHONET.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -205,11 +205,11 @@ diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html index 77ae3dc0..b4a7a5c3 100644 --- a/reference/ab_from_text.html +++ b/reference/ab_from_text.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -289,11 +289,11 @@ diff --git a/reference/ab_property.html b/reference/ab_property.html index 341cf1c4..e90c239b 100644 --- a/reference/ab_property.html +++ b/reference/ab_property.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -505,11 +505,11 @@ diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html index 5199c88e..8d47d5a3 100644 --- a/reference/add_custom_antimicrobials.html +++ b/reference/add_custom_antimicrobials.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -284,11 +284,11 @@ diff --git a/reference/age.html b/reference/age.html index 675f616c..f46467ed 100644 --- a/reference/age.html +++ b/reference/age.html @@ -10,7 +10,7 @@ AMR (for R) - 1.8.2.9060 + 1.8.2.9061 @@ -195,16 +195,16 @@ df #> birth_date age age_exact age_at_y2k -#> 1 1989-04-30 33 33.61370 10 -#> 2 1989-10-13 33 33.15890 10 -#> 3 1963-05-01 59 59.61096 36 -#> 4 1966-07-25 56 56.37808 33 -#> 5 1958-10-27 64 64.12055 41 -#> 6 1941-11-22 81 81.04932 58 -#> 7 1953-03-22 69 69.72055 46 -#> 8 1945-01-30 77 77.86027 54 -#> 9 1932-10-13 90 90.15890 67 -#> 10 1953-07-03 69 69.43836 46 +#> 1 1989-09-25 33 33.21096 10 +#> 2 1941-12-25 80 80.96164 58 +#> 3 1987-05-25 35 35.54795 12 +#> 4 1957-06-15 65 65.49041 42 +#> 5 1984-05-25 38 38.54795 15 +#> 6 1937-04-16 85 85.65479 62 +#> 7 1949-06-01 73 73.52877 50 +#> 8 1961-04-18 61 61.64932 38 +#> 9 1965-05-20 57 57.56164 34 +#> 10 1982-06-09 40 40.50685 17
vignettes/datasets.Rmd
datasets.Rmd
The development of this package is part of, related to, or made possible by:
The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:
This version will eventually become v2.0! We’re happy to reach a new major milestone soon!
units
ab_ddd(..., units = "...")
ab_ddd_units()
as.rsi()
eucast_rules()
AMR
NA
as.rsi(as.disk(NA), ...)
as.mic()
as.disk()
styler
-This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm).
This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm).
These have become the gold standard for international drug utilisation monitoring and research.
The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://www.whocc.no/copyright_disclaimer/.