This is basically it for the cleaning, time to start the data inclusion.
Time for the analysis.
head(my_TB_data) #> rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin -#> 1 I R I I S R -#> 2 I R R S S I -#> 3 I R S R R R -#> 4 R R I R I R -#> 5 R R R R R S -#> 6 S R S S R S +#> 1 I I I R S S +#> 2 S R R R R S +#> 3 I R S I I S +#> 4 I S S S S R +#> 5 S I R I R R +#> 6 S I I I I R #> kanamycin -#> 1 I -#> 2 I +#> 1 S +#> 2 R #> 3 S -#> 4 S +#> 4 I #> 5 R -#> 6 S
We can now add the interpretation of MDR-TB to our data set. You can use:
@@ -438,40 +438,40 @@ Unique: 5 1 Mono-resistant -3251 -65.02% -3251 -65.02% +3214 +64.28% +3214 +64.28% 2 Negative -971 -19.42% -4222 -84.44% +1016 +20.32% +4230 +84.60% 3 Multi-drug-resistant -468 -9.36% -4690 -93.80% +424 +8.48% +4654 +93.08% 4 Poly-resistant -226 -4.52% -4916 -98.32% +247 +4.94% +4901 +98.02% 5 Extensively drug-resistant -84 -1.68% +99 +1.98% 5000 100.00% diff --git a/articles/PCA.html b/articles/PCA.html index 2e9186be..3eca9b91 100644 --- a/articles/PCA.html +++ b/articles/PCA.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -290,7 +290,7 @@ function: #> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales" #> Importance of components: #> PC1 PC2 PC3 PC4 PC5 PC6 PC7 -#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 +#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
#> Groups (n=4, named as 'order'): diff --git a/articles/SPSS.html b/articles/SPSS.html index 7250d724..82dfe7d3 100644 --- a/articles/SPSS.html +++ b/articles/SPSS.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -178,7 +178,7 @@ Dr. Matthijs Berends - 20 March 2023 + 14 April 2023 Source: vignettes/SPSS.Rmd SPSS.Rmd @@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed R has a huge community. Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 484 734 +online community for programmers. At the time of writing, 486 808 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 78b2123f..e80bddaf 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -322,7 +322,7 @@ Longest: 40 8 -Staphylococcus capitis +Staphylococcus capitis urealyticus 8 1.6% 434 diff --git a/articles/datasets.html b/articles/datasets.html index 87a380d9..4ed271ab 100644 --- a/articles/datasets.html +++ b/articles/datasets.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -176,7 +176,7 @@ Data sets for download / own use - 20 March 2023 + 14 April 2023 Source: vignettes/datasets.Rmd datasets.Rmd @@ -197,7 +197,7 @@ of the data sets look like. microorganisms: Full Microbial Taxonomy -A data set with 52 142 rows and 22 columns, containing the following +A data set with 52 149 rows and 22 columns, containing the following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, @@ -206,7 +206,7 @@ column names:mo, fullname, status, kingdomgbif_renamed_to, prevalence, and snomed. This data set is in R available as microorganisms, after you load the AMR package. -It was last updated on 26 February 2023 20:26:58 UTC. Find more info +It was last updated on 14 April 2023 09:12:26 UTC. Find more info about the structure of this data set here. Direct download links: @@ -283,7 +283,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: Bacteria -36 476 +36 483 Fungi diff --git a/articles/index.html b/articles/index.html index ef34b24a..1280603f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html index c45f3b59..c02447f5 100644 --- a/articles/resistance_predict.html +++ b/articles/resistance_predict.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -251,7 +251,7 @@ resistance and the standard error below and above the estimation: #> 8 2009 0.0164 NA NA 61 0.0164 0.106 #> 9 2010 0.0566 NA NA 53 0.0566 0.116 #> 10 2011 0.183 NA NA 93 0.183 0.127 -#> # … with 22 more rows +#> # ℹ 22 more rows The function plot is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions: diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html index 772e26f0..4a92ccbf 100644 --- a/articles/welcome_to_AMR.html +++ b/articles/welcome_to_AMR.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/authors.html b/authors.html index 9e411ff6..5428c143 100644 --- a/authors.html +++ b/authors.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/index.html b/index.html index 6bb51f2a..71a8410e 100644 --- a/index.html +++ b/index.html @@ -42,7 +42,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/news/index.html b/news/index.html index c06e5008..6c37a9da 100644 --- a/news/index.html +++ b/news/index.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -142,11 +142,12 @@ -AMR 2.0.0.9004 +AMR 2.0.0.9005 -Changed +Changed formatting fix for sir_interpretation_history() +Fixed some WHONET codes for microorganisms diff --git a/pkgdown.yml b/pkgdown.yml index e364bda5..f3c6c71b 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: 2023-03-20T21:06Z +last_built: 2023-04-14T09:18Z 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 30e7c450..9eacf34a 100644 --- a/reference/AMR-deprecated.html +++ b/reference/AMR-deprecated.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/reference/AMR-options.html b/reference/AMR-options.html index 85e477df..f26be061 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 diff --git a/reference/AMR.html b/reference/AMR.html index 0826775c..f1efa81b 100644 --- a/reference/AMR.html +++ b/reference/AMR.html @@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131 and doi:10.33612/diss.192486375 ). -After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. +After installing this package, R knows ~52 000 microorganisms (updated december 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.">The AMR Package — AMR • AMR (for R)Data Set with 5 910 Common Microorganism Codes — microorganisms.codes • AMR (for R)Data Set with 5 751 Common Microorganism Codes — microorganisms.codes • AMR (for R) @@ -10,7 +10,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -137,7 +137,7 @@ - Data Set with 5 910 Common Microorganism Codes + Data Set with 5 751 Common Microorganism Codes Source: R/data.R microorganisms.codes.Rd @@ -153,7 +153,7 @@ Format - A tibble with 5 910 observations and 2 variables:code Commonly used code of a microorganism + A tibble with 5 751 observations and 2 variables:code Commonly used code of a microorganism mo ID of the microorganism in the microorganisms data set @@ -168,7 +168,7 @@ Examples microorganisms.codes -#> # A tibble: 5,910 × 2 +#> # A tibble: 5,751 × 2 #> code mo #> <chr> <mo> #> 1 _FAM_A- B_GRAMN @@ -181,7 +181,7 @@ #> 8 _FAM_AS F_FUNGUS #> 9 _FAM_AT UNKNOWN #> 10 _FAM_AV UNKNOWN -#> # … with 5,900 more rows +#> # ℹ 5,741 more rows
vignettes/SPSS.Rmd
SPSS.Rmd
R has a huge community.
Many R users just ask questions on websites like StackOverflow.com, the largest -online community for programmers. At the time of writing, 484 734 +online community for programmers. At the time of writing, 486 808 R-related questions have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of diff --git a/articles/WHONET.html b/articles/WHONET.html index 78b2123f..e80bddaf 100644 --- a/articles/WHONET.html +++ b/articles/WHONET.html @@ -38,7 +38,7 @@ AMR (for R) - 2.0.0.9004 + 2.0.0.9005 @@ -322,7 +322,7 @@ Longest: 40
vignettes/datasets.Rmd
datasets.Rmd
microorganisms
A data set with 52 142 rows and 22 columns, containing the following +
A data set with 52 149 rows and 22 columns, containing the following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, @@ -206,7 +206,7 @@ column names:mo, fullname, status, kingdomgbif_renamed_to, prevalence, and snomed.
This data set is in R available as microorganisms, after you load the AMR package.
AMR
It was last updated on 26 February 2023 20:26:58 UTC. Find more info +
It was last updated on 14 April 2023 09:12:26 UTC. Find more info about the structure of this data set here.
Direct download links:
The function plot is available in base R, and can be extended by other packages to depend the output based on the type of input. We extended its function to cope with resistance predictions:
plot
sir_interpretation_history()
R/data.R
microorganisms.codes.Rd
A tibble with 5 910 observations and 2 variables:
code Commonly used code of a microorganism
code
A tibble with 5 751 observations and 2 variables:
mo ID of the microorganism in the microorganisms data set
mo
microorganisms.codes -#> # A tibble: 5,910 × 2 +#> # A tibble: 5,751 × 2 #> code mo #> <chr> <mo> #> 1 _FAM_A- B_GRAMN @@ -181,7 +181,7 @@ #> 8 _FAM_AS F_FUNGUS #> 9 _FAM_AT UNKNOWN #> 10 _FAM_AV UNKNOWN -#> # … with 5,900 more rows +#> # ℹ 5,741 more rows