From 1ee710c8616e2d99782a407d0e2aabfc0bea2f41 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Tue, 15 Jan 2019 16:51:49 +0100 Subject: [PATCH] resistance predict --- R/resistance_predict.R | 8 +- docs/index.html | 26 +++-- docs/news/index.html | 211 ++++++++--------------------------------- docs/pkgdown.yml | 2 +- 4 files changed, 54 insertions(+), 193 deletions(-) diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 50654f9b..caf0d217 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -335,9 +335,9 @@ ggplot_rsi_predict <- function(x, main = paste("Resistance prediction of", attri ggplot2::geom_col() + ggplot2::geom_errorbar(ggplot2::aes(ymin = se_min, ymax = se_max)) + scale_y_percent() + - labs(title = main, - y = paste0("Percentage (", ylab, ")"), - x = "Year", - caption = paste0("(model: ", attributes(x)$model_title, ")")) + ggplot2::labs(title = main, + y = paste0("Percentage (", ylab, ")"), + x = "Year", + caption = paste0("(model: ", attributes(x)$model_title, ")")) ) } diff --git a/docs/index.html b/docs/index.html index 2efd8420..d5063da5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -221,7 +221,7 @@

Get this package

This package is available on the official R network (CRAN). Install this package in R with:

-
install.packages("AMR")
+
install.packages("AMR")

It will be downloaded and installed automatically.

@@ -245,17 +245,17 @@ Overview of functions

The AMR package basically does four important things:

    -
  1. -

    It cleanses existing data, by transforming it to reproducible and profound classes, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:

    +
  2. It cleanses existing data, by transforming it to reproducible and profound classes, making the most efficient use of R. These functions all use artificial intelligence to guess results that you would expect:
    3. +
- -
  • -

    It enhances existing data and adds new data from data sets included in this package.

    +
      +
    1. It enhances existing data and adds new data from data sets included in this package.
      2. +
    • Use eucast_rules() to apply EUCAST expert rules to isolates.
    • Use first_isolate() to identify the first isolates of every patient using guidelines from the CLSI (Clinical and Laboratory Standards Institute). @@ -267,9 +267,9 @@
    • The data set microorganisms contains the complete taxonomic tree of more than 18,000 microorganisms (bacteria, fungi/yeasts and protozoa). Furthermore, the colloquial name and Gram stain are available, which enables resistance analysis of e.g. different antibiotics per Gram stain. The package also contains functions to look up values in this data set like mo_genus(), mo_family(), mo_gramstain() or even mo_phylum(). As they use as.mo() internally, they also use artificial intelligence. For example, mo_genus("MRSA") and mo_genus("S. aureus") will both return "Staphylococcus". They also come with support for German, Dutch, Spanish, Italian, French and Portuguese. These functions can be used to add new variables to your data.
    • The data set antibiotics contains the ATC code, LIS codes, official name, trivial name and DDD of both oral and parenteral administration. It also contains a total of 298 trade names. Use functions like ab_name() and ab_tradenames() to look up values. The ab_* functions use as.atc() internally so they support AI to guess your expected result. For example, ab_name("Fluclox"), ab_name("Floxapen") and ab_name("J01CF05") will all return "Flucloxacillin". These functions can again be used to add new variables to your data.
    -
    • -
  • -

    It analyses the data with convenient functions that use well-known methods.

    +
      +
    1. It analyses the data with convenient functions that use well-known methods.
      2. +
    -
    • -
  • -

    It teaches the user how to use all the above actions.

    +
      +
    1. It teaches the user how to use all the above actions.
      2. +
    • The package contains extensive help pages with many examples.
    • It also contains an example data set called septic_patients. This data set contains: @@ -290,8 +290,6 @@
    • - -

    diff --git a/docs/news/index.html b/docs/news/index.html index 3e0c888e..e1d1981c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -229,53 +229,33 @@

    Changed

    @@ -603,21 +496,15 @@ New

    - -
  • Determining bacterial ID: -
      +
    • Determining bacterial ID:
    • New functions as.bactid and is.bactid to transform/ look up microbial ID’s.
    • The existing function guess_bactid is now an alias of as.bactid
    • New Becker classification for Staphylococcus to categorise them into Coagulase Negative Staphylococci (CoNS) and Coagulase Positve Staphylococci (CoPS)
    • New Lancefield classification for Streptococcus to categorise them into Lancefield groups
      • -
    -
  • For convience, new descriptive statistical functions kurtosis and skewness that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
  • Function g.test to perform the Χ2 distributed G-test, which use is the same as chisq.test
    • -
  • -Function ratio to transform a vector of values to a preset ratio - -
  • Support for Addins menu in RStudio to quickly insert %in% or %like% (and give them keyboard shortcuts), or to view the datasets that come with this package
  • Function p.symbol to transform p values to their related symbols: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  • Functions clipboard_import and clipboard_export as helper functions to quickly copy and paste from/to software like Excel and SPSS. These functions use the clipr package, but are a little altered to also support headless Linux servers (so you can use it in RStudio Server)
    • -
  • New for frequency tables (function freq): -
      +
    • New for frequency tables (function freq):
    • A vignette to explain its usage
    • Support for rsi (antimicrobial resistance) to use as input
    • Support for table to use as input: freq(table(x, y)) @@ -668,8 +545,6 @@
    • Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)
    • Possibility to globally set the default for the amount of items to print, with options(max.print.freq = n) where n is your preset value
    -
    • -

    @@ -691,27 +566,21 @@
  • Small improvements to the microorganisms dataset (especially for Salmonella) and the column bactid now has the new class "bactid"
    • -
  • Combined MIC/RSI values will now be coerced by the rsi and mic functions: - -
  • Now possible to coerce MIC values with a space between operator and value, i.e. as.mic("<= 0.002") now works
  • Classes rsi and mic do not add the attribute package.version anymore
  • Added "groups" option for atc_property(..., property). It will return a vector of the ATC hierarchy as defined by the WHO. The new function atc_groups is a convenient wrapper around this.
  • Build-in host check for atc_property as it requires the host set by url to be responsive
  • Improved first_isolate algorithm to exclude isolates where bacteria ID or genus is unavailable
  • Fix for warning hybrid evaluation forced for row_number (924b62) from the dplyr package v0.7.5 and above
    • -
  • Support for empty values and for 1 or 2 columns as input for guess_bactid (now called as.bactid) -
      +
    • Support for empty values and for 1 or 2 columns as input for guess_bactid (now called as.bactid)
    • So yourdata %>% select(genus, species) %>% as.bactid() now also works
      • -
    -
  • Other small fixes

    • @@ -719,14 +588,11 @@

    Other

    @@ -745,13 +611,10 @@
  • Function guess_bactid to determine the ID of a microorganism based on genus/species or known abbreviations like MRSA
  • Function guess_atc to determine the ATC of an antibiotic based on name, trade name, or known abbreviations
  • Function freq to create frequency tables, with additional info in a header
    • -
  • Function MDRO to determine Multi Drug Resistant Organisms (MDRO) with support for country-specific guidelines. - -
  • New algorithm to determine weighted isolates, can now be "points" or "keyantibiotics", see ?first_isolate
  • New print format for tibbles and data.tables
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 31227eab..3c396dbb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.3.1 +pandoc: 1.17.2 pkgdown: 1.3.0 pkgdown_sha: ~ articles: