diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 60a80507..be8dc0fe 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -33,7 +33,11 @@ variables: before_script: - apt-get update -qq # install dependencies for packages - - apt-get install -y locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc pandoc-citeproc r-base > /dev/null + - apt-get install -y locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev r-base > /dev/null + # recent pandoc + - wget https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb + - dpkg -i pandoc*.deb + - rm pandoc*.deb # set R system language - echo "LC_ALL=en_US.UTF-8" >> /etc/environment - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen diff --git a/DESCRIPTION b/DESCRIPTION index af59cfc0..d98e45ab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR Version: 0.5.0.9017 -Date: 2019-02-09 +Date: 2019-02-10 Title: Antimicrobial Resistance Analysis Authors@R: c( person( diff --git a/docs/index.html b/docs/index.html index a931a8d1..e7fbbee4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -183,9 +183,9 @@
-
+

-AMR (for R) +AMR (for R)

(TLDR - to find out how to conduct AMR analysis, please continue reading here to get started.

@@ -238,15 +238,15 @@

Latest released version

This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:

- +

It will be downloaded and installed automatically. For RStudio, click on the menu Tools > Install Packages… and then type in “AMR” and press Install.

Latest development version

The latest and unpublished development version can be installed with (precaution: may be unstable):

-
install.packages("devtools")
-devtools::install_gitlab("msberends/AMR")
+
install.packages("devtools")
+devtools::install_gitlab("msberends/AMR")
@@ -257,9 +257,9 @@

Short introduction

-
+

-WHONET / EARS-Net

+WHONET / EARS-Net

We support WHONET and EARS-Net data. Exported files from WHONET can be imported into R and can be analysed easily using this package. For education purposes, we created an example data set WHONET with the exact same structure and a WHONET export file. Furthermore, this package also contains a data set antibiotics with all EARS-Net antibiotic abbreviations, and knows almost all WHONET abbreviations for microorganisms. When using WHONET data as input for analysis, all input parameters will be set automatically.

Read our tutorial about how to work with WHONET data here.

diff --git a/docs/news/index.html b/docs/news/index.html index d91d6d45..d65484c8 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -225,9 +225,9 @@
-
+

-AMR 0.5.0.90xx Unreleased +AMR 0.5.0.90xx Unreleased

Note: this is the development version, which will eventually be released as AMR 0.6.0.

@@ -245,14 +245,14 @@

  • All ab_* functions are deprecated and replaced by atc_* functions:

    - -These functions use as.atc() internally. The old atc_property has been renamed atc_online_property(). This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class atc or must be coerable to this class. Properties of these classes should start with the same class name, analogous to as.mo() and e.g. mo_genus.
    • + +These functions use as.atc() internally. The old atc_property has been renamed atc_online_property(). This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class atc or must be coerable to this class. Properties of these classes should start with the same class name, analogous to as.mo() and e.g. mo_genus.
  • New website: https://msberends.gitlab.io/AMR (built with the great pkgdown)
    • -
    +

    -AMR 0.5.0 2018-11-30 +AMR 0.5.0 2018-11-30

    @@ -433,10 +433,10 @@ These functions use as.atc()
  • Fewer than 3 characters as input for as.mo will return NA

  • Function as.mo (and all mo_* wrappers) now supports genus abbreviations with “species” attached

    -
    as.mo("E. species")        # B_ESCHR
-mo_fullname("E. spp.")     # "Escherichia species"
-as.mo("S. spp")            # B_STPHY
-mo_fullname("S. species")  # "Staphylococcus species"
    +
    as.mo("E. species")        # B_ESCHR
+mo_fullname("E. spp.")     # "Escherichia species"
+as.mo("S. spp")            # B_STPHY
+mo_fullname("S. species")  # "Staphylococcus species"
  • Added parameter combine_IR (TRUE/FALSE) to functions portion_df and count_df, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)
  • Fix for portion_*(..., as_percent = TRUE) when minimal number of isolates would not be met
    • @@ -449,15 +449,15 @@ These functions use as.atc()

    -
    +

    -AMR 0.4.0 2018-10-01 +AMR 0.4.0 2018-10-01

    @@ -537,18 +537,18 @@ These functions use as.atc()

    They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:

    -
    mo_gramstain("E. coli")
-# [1] "Gram negative"
-mo_gramstain("E. coli", language = "de") # German
-# [1] "Gramnegativ"
-mo_gramstain("E. coli", language = "es") # Spanish
-# [1] "Gram negativo"
-mo_fullname("S. group A", language = "pt") # Portuguese
-# [1] "Streptococcus grupo A"
    +
    mo_gramstain("E. coli")
+# [1] "Gram negative"
+mo_gramstain("E. coli", language = "de") # German
+# [1] "Gramnegativ"
+mo_gramstain("E. coli", language = "es") # Spanish
+# [1] "Gram negativo"
+mo_fullname("S. group A", language = "pt") # Portuguese
+# [1] "Streptococcus grupo A"

    Furthermore, former taxonomic names will give a note about the current taxonomic name:

    - +
  • Functions count_R, count_IR, count_I, count_SI and count_S to selectively count resistant or susceptible isolates

    • @@ -651,9 +651,9 @@ These functions use as.atc()
    -
    +

    -AMR 0.3.0 2018-08-14 +AMR 0.3.0 2018-08-14

    @@ -758,7 +758,7 @@ These functions use as.atc() -
  • Now possible to coerce MIC values with a space between operator and value, i.e. as.mic("<= 0.002") now works
    • +
  • 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
    • @@ -788,9 +788,9 @@ These functions use as.atc()

    -
    +

    -AMR 0.2.0 2018-05-03 +AMR 0.2.0 2018-05-03

    @@ -846,9 +846,9 @@ These functions use as.atc()

    -
    +

    -AMR 0.1.1 2018-03-14 +AMR 0.1.1 2018-03-14

    • @@ -859,9 +859,9 @@ These functions use as.atc()
    • Added barplots for rsi and mic classes
    -
    +

    -AMR 0.1.0 2018-02-22 +AMR 0.1.0 2018-02-22

    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index ac0898dd..20485bdb 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.3.1 +pandoc: '2.6' pkgdown: 1.3.0 pkgdown_sha: ~ articles: