diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 94a609b1..8c023b03 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -56,16 +56,18 @@ jobs: - {os: windows-latest, r: 'devel', allowfail: false} - {os: windows-latest, r: 'release', allowfail: false} - {os: windows-latest, r: 'oldrel', allowfail: false} - - {os: ubuntu-16.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: 'oldrel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.4', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - # - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - # older R versions cannot be tested, since tidyverse only supports last 4 R x.x versions + - {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} @@ -80,13 +82,14 @@ jobs: - uses: r-lib/actions/setup-pandoc@master - name: Query dependencies + if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' run: | install.packages('remotes') saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} - name: Cache R packages - if: runner.os != 'Windows' + if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' uses: actions/cache@v1 with: path: ${{ env.R_LIBS_USER }} @@ -94,7 +97,7 @@ jobs: restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3- - name: Install Linux dependencies - if: runner.os == 'Linux' + if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' env: RHUB_PLATFORM: linux-x86_64-ubuntu-gcc run: | @@ -108,6 +111,7 @@ jobs: brew install mariadb-connector-c - name: Install dependencies + if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' run: | remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") @@ -116,15 +120,25 @@ jobs: - name: Session info run: | options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) + utils::sessionInfo() + as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - name: Run R CMD check + if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' env: _R_CHECK_CRAN_INCOMING_: false run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") shell: Rscript {0} + + - name: Run R CMD check on older R versions + if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' + env: + _R_CHECK_CRAN_INCOMING_: false + _R_CHECK_FORCE_SUGGESTS_: false + run: | + ls -lh + R CMD check data-raw/AMR_*.tar.gz - name: Show testthat output if: always() diff --git a/DESCRIPTION b/DESCRIPTION index e40deb16..982cbec9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.4.0.9052 -Date: 2020-12-28 +Version: 1.4.0.9053 +Date: 2020-12-29 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 3adf7533..0c10e5a8 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.4.0.9052 -## Last updated: 28 December 2020 +# AMR 1.4.0.9053 +## Last updated: 29 December 2020 ### New * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`): diff --git a/R/ab_from_text.R b/R/ab_from_text.R index 948922da..813472e8 100644 --- a/R/ab_from_text.R +++ b/R/ab_from_text.R @@ -33,7 +33,7 @@ #' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name". #' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words. #' @param ... arguments passed on to [as.ab()] -#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. +#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. #' #' ## Argument `type` #' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling. diff --git a/R/mo.R b/R/mo.R index b90954a0..4aeaf127 100755 --- a/R/mo.R +++ b/R/mo.R @@ -2006,5 +2006,3 @@ repair_reference_df <- function(reference_df) { reference_df[, "mo"] <- as.mo(reference_df[, "mo", drop = TRUE]) reference_df } - -pkg_env <- new.env(hash = FALSE) diff --git a/R/mo_property.R b/R/mo_property.R index 6599ca3d..9ddbb4dd 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -433,12 +433,11 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) { stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.") } - # show used version number once per session - if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) { + # show used version number once + if (message_not_thrown_before("intrinsic_resistant_version")) { message_("Determining intrinsic resistance based on ", - format_eucast_version_nr(3.2, FALSE), ". ", - font_bold("This note is shown only once per session.")) - options(AMR_intrinsic_resistance_note = "shown") + format_eucast_version_nr(3.2, markdown = FALSE), ".") + remember_thrown_message("intrinsic_resistant_version") } # runs against internal vector: INTRINSIC_R (see zzz.R) diff --git a/R/zzz.R b/R/zzz.R index ef6fd486..4f75c05f 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -23,6 +23,9 @@ # how to conduct AMR analysis: https://msberends.github.io/AMR/ # # ==================================================================== # +# set up package environment, used by numerous AMR functions +pkg_env <- new.env(hash = FALSE) + .onLoad <- function(libname, pkgname) { assign(x = "AB_lookup", diff --git a/README.md b/README.md index efeca949..9357c481 100755 --- a/README.md +++ b/README.md @@ -2,8 +2,11 @@ # `AMR` (for R) -[![CRAN_Badge](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.R-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.R-project.org/package=AMR) -[![CodeCov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR/branch/master) +[![CRAN](https://www.r-pkg.org/badges/version-ago/AMR)](https://cran.r-project.org/package=AMR) +[![CRANlogs](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](https://cran.r-project.org/package=AMR) +![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master) +[![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr) +[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master) diff --git a/data-raw/AMR_1.4.0.9053.tar.gz b/data-raw/AMR_1.4.0.9053.tar.gz new file mode 100644 index 00000000..c6ed62df Binary files /dev/null and b/data-raw/AMR_1.4.0.9053.tar.gz differ diff --git a/docs/404.html b/docs/404.html index e87d8651..98cbe37e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index c139382d..bc166182 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index 1b29aeb1..2386ed8a 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 @@ -193,7 +193,7 @@

How to conduct AMR analysis

Matthijs S. Berends

-

26 December 2020

+

29 December 2020

Source: vignettes/AMR.Rmd @@ -202,7 +202,7 @@ -

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 26 December 2020.

+

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 29 December 2020.

Introduction

@@ -233,21 +233,21 @@ -2020-12-26 +2020-12-29 abcd Escherichia coli S S -2020-12-26 +2020-12-29 abcd Escherichia coli S R -2020-12-26 +2020-12-29 efgh Escherichia coli R @@ -352,9 +352,9 @@ -2011-10-28 -I1 -Hospital A +2014-02-24 +H4 +Hospital D Staphylococcus aureus R S @@ -363,41 +363,19 @@ M -2011-06-05 -G5 -Hospital A -Escherichia coli +2017-04-27 +Q3 +Hospital B +Staphylococcus aureus +S R -S -S -S -M - - -2014-05-12 -X7 -Hospital D -Streptococcus pneumoniae -S -S R S F - -2011-02-23 -K5 -Hospital A -Staphylococcus aureus -S -S -S -S -M - -2017-09-20 -T5 +2013-03-12 +Q4 Hospital B Escherichia coli S @@ -407,15 +385,37 @@ F -2017-02-10 -Y6 -Hospital D +2013-03-24 +H9 +Hospital A Escherichia coli -I +R S S S -F +M + + +2017-03-11 +M1 +Hospital A +Streptococcus pneumoniae +R +S +S +S +M + + +2011-12-21 +M5 +Hospital A +Streptococcus pneumoniae +S +S +S +S +M @@ -449,16 +449,16 @@ Longest: 1

1 M -10,426 -52.13% -10,426 -52.13% +10,444 +52.22% +10,444 +52.22% 2 F -9,574 -47.87% +9,556 +47.78% 20,000 100.00% @@ -503,7 +503,7 @@ Longest: 1

# NOTE: Using column 'bacteria' as input for `col_mo`. # NOTE: Using column 'date' as input for `col_date`. # NOTE: Using column 'patient_id' as input for `col_patient_id`.
-

So only 28.4% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

+

So only 28.3% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

 data_1st <- data %>% 
   filter(first == TRUE)
@@ -515,7 +515,7 @@ Longest: 1

First weighted isolates

-

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient F3, sorted on date:

+

We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Z4, sorted on date:

@@ -531,43 +531,43 @@ Longest: 1

- - + + - - + + - - + + + - - + - - + + - + - - + + - + @@ -575,19 +575,19 @@ Longest: 1

- - + + + - - + - - + + @@ -597,51 +597,51 @@ Longest: 1

- - + + - - - + + + - - + + - + - - + + - - + + - - + + - - + - + +
isolate
12010-01-17F32010-07-01Z4 B_ESCHR_COLI S SRRSS TRUE
22010-03-13F32010-08-01Z4 B_ESCHR_COLII SSSR S FALSE
32010-04-21F32010-08-18Z4 B_ESCHR_COLI RSI R S FALSE
42010-06-24F32010-10-16Z4 B_ESCHR_COLISR S S S
52010-08-02F32010-12-23Z4 B_ESCHR_COLIR S SSSR FALSE
62010-08-14F32010-12-25Z4 B_ESCHR_COLI S S
72010-10-06F32011-01-07Z4 B_ESCHR_COLISSSRRR S FALSE
82010-10-17F32011-01-30Z4 B_ESCHR_COLI RRS S S FALSE
92010-11-17F32011-05-19Z4 B_ESCHR_COLIRI S SRS FALSE
102011-02-21F32011-06-21Z4 B_ESCHR_COLIRRS S RTRUESFALSE
-

Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

+

Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The key_antibiotics() function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.

If a column exists with a name like ‘key(…)ab’ the first_isolate() function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:

 data <- data %>% 
@@ -665,46 +665,46 @@ Longest: 1

 
 
 1
-2010-01-17
-F3
+2010-07-01
+Z4
 B_ESCHR_COLI
 S
 S
-R
-R
+S
+S
 TRUE
 TRUE
 
 
 2
-2010-03-13
-F3
+2010-08-01
+Z4
 B_ESCHR_COLI
+I
 S
-S
-S
+R
 S
 FALSE
 TRUE
 
 
 3
-2010-04-21
-F3
+2010-08-18
+Z4
 B_ESCHR_COLI
 R
-S
+I
 R
 S
 FALSE
-TRUE
+FALSE
 
 
 4
-2010-06-24
-F3
+2010-10-16
+Z4
 B_ESCHR_COLI
-S
+R
 S
 S
 S
@@ -713,47 +713,47 @@ Longest: 1

 
 
 5
-2010-08-02
-F3
+2010-12-23
+Z4
 B_ESCHR_COLI
+R
 S
 S
-S
-S
-FALSE
+R
 FALSE
+TRUE
 
 
 6
-2010-08-14
-F3
+2010-12-25
+Z4
 B_ESCHR_COLI
 S
 S
 S
 S
 FALSE
-FALSE
+TRUE
 
 
 7
-2010-10-06
-F3
+2011-01-07
+Z4
 B_ESCHR_COLI
-S
-S
-S
+R
+R
+R
 S
 FALSE
-FALSE
+TRUE
 
 
 8
-2010-10-17
-F3
+2011-01-30
+Z4
 B_ESCHR_COLI
 R
-R
+S
 S
 S
 FALSE
@@ -761,36 +761,36 @@ Longest: 1

 
 
 9
-2010-11-17
-F3
+2011-05-19
+Z4
 B_ESCHR_COLI
+S
+S
 R
-I
-S
 S
 FALSE
-FALSE
+TRUE
 
 
 10
-2011-02-21
-F3
+2011-06-21
+Z4
 B_ESCHR_COLI
-R
-R
+S
 S
 R
-TRUE
-TRUE
+S
+FALSE
+FALSE
 
 
 
-
Instead of 2, now 6 isolates are flagged. In total, 78.5% of all isolates are marked ‘first weighted’ - 50.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

+
Instead of 1, now 8 isolates are flagged. In total, 79.0% of all isolates are marked ‘first weighted’ - 50.7% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

 
As with filter_first_isolate(), there’s a shortcut for this new algorithm too:

 
 data_1st <- data %>% 
   filter_first_weighted_isolate()

-
So we end up with 15,695 isolates for analysis.

+
So we end up with 15,805 isolates for analysis.

 
We can remove unneeded columns:

 
 data_1st <- data_1st %>% 
@@ -800,7 +800,6 @@ Longest: 1

 head(data_1st)

 -@@ -816,7 +815,6 @@ Longest: 1

-
@@ -833,10 +831,9 @@ Longest: 1

-
-
-
-
+
+
+
@@ -849,9 +846,38 @@ Longest: 1

-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -865,67 +891,33 @@ Longest: 1

-
-
-
-
+
+
+
-
-
-
+
+
+
-
-
-
+
+
-
+
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
@@ -949,8 +941,8 @@ Longest: 1
data_1st %>% freq(genus, species)
Frequency table
Class: character

-Length: 15,695

-Available: 15,695 (100%, NA: 0 = 0%)

+Length: 15,805

+Available: 15,805 (100%, NA: 0 = 0%)

 Unique: 4
Shortest: 16

 Longest: 24

@@ -968,32 +960,32 @@ Longest: 24

-
+
-
+
-
-
-
-
+
+
+
+
-
-
-
-
+
+
+
+
-
-
-
+
+
+
@@ -1020,33 +1012,33 @@ Longest: 24

-
-
-
+
+
+
-
-
-
+
+
+
-
+
-
+
-
+
-
+
@@ -1054,16 +1046,16 @@ Longest: 24

-
-
+
+
-
-
-
-
+
+
+
+

 

 
 
 

 
 
 

 date
 patient_id
 hospital
 

 
 
12011-10-28I1Hospital A2014-02-24H4Hospital D
 B_STPHY_AURS
 R
 S
 TRUE
 

 
22011-06-05G52017-04-27Q3Hospital BB_STPHY_AURSRRRSFGram-positiveStaphylococcusaureusTRUE
2013-03-12Q4Hospital BB_ESCHR_COLISSRSFGram-negativeEscherichiacoliTRUE
2013-03-24H9
 Hospital A
 B_ESCHR_COLI
 R
 TRUE
 

 
32014-05-12X7Hospital D2017-03-11M1Hospital A
 B_STRPT_PNMNSS
 R
 RFSRM
 Gram-positive
 Streptococcus
 pneumoniae
 TRUE
 

 
42011-02-23K52011-12-21M5
 Hospital AB_STPHY_AURSB_STRPT_PNMN
 S
 S
 SSMGram-positiveStaphylococcusaureusTRUE
52017-09-20T5Hospital BB_ESCHR_COLISS
 RSFGram-negativeEscherichiacoliTRUE
72017-12-17Z3Hospital BB_ESCHR_COLISSSSFGram-negativeEscherichiacoliMGram-positiveStreptococcuspneumoniae
 TRUE
 

 
 
 
 
 
 
1
 Escherichia coli
 7,82849.88%49.53%
 7,82849.88%49.53%
 

 

 2
 Staphylococcus aureus3,97725.34%11,80575.22%3,96325.07%11,79174.60%
 

 

 3
 Streptococcus pneumoniae2,32014.78%14,12590.00%2,39215.13%14,18389.74%
 

 

 4
 Klebsiella pneumoniae1,57010.00%15,6951,62210.26%15,805
 100.00%
 

 
 

 E. coli
 AMX3731275382237772453806
 7828
 

 

 E. coli
 AMC6146297138561592781391
 7828
 

 

 E. coli
 CIP59185997
 019101831
 7828
 

 

 E. coli
 GEN70876984
 0741844
 7828
 

 

 AMX
 0
 01570157016221622
 

 

 K. pneumoniae
 AMC12315728215701271632881622
 

 
 

@@ -1072,7 +1064,7 @@ Longest: 24

 data_1st %>% 
   select(bacteria, fluoroquinolones()) %>% 
   bug_drug_combinations()
-
# Selecting fluoroquinolones: 'CIP' (ciprofloxacin)
+
# Selecting fluoroquinolones: column 'CIP' (ciprofloxacin)
@@ -1086,34 +1078,34 @@ Longest: 24

- + - + - + - - + + - + - - + + - + - - + +
mo
E. coli CIP59185997 019101831 7828
K. pneumoniae CIP11911266 037915703561622
S. aureus CIP30453017 093239779463963
S. pneumoniae CIP17851844 053523205482392
@@ -1126,7 +1118,7 @@ Longest: 24

As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R(), equal to resistance()) and susceptibility as the proportion of S and I (proportion_SI(), equal to susceptibility()). These functions can be used on their own:

 data_1st %>% resistance(AMX)
-# [1] 0.536604
+# [1] 0.5358431

Or can be used in conjuction with group_by() and summarise(), both from the dplyr package:

 data_1st %>% 
@@ -1141,19 +1133,19 @@ Longest: 24

 
 
 Hospital A
-0.5429950
+0.5273258
 
 
 Hospital B
-0.5429998
+0.5421512
 
 
 Hospital C
-0.5283993
+0.5394139
 
 
 Hospital D
-0.5222153
+0.5350195
 
 
 
@@ -1173,23 +1165,23 @@ Longest: 24

 
 
 Hospital A
-0.5429950
-4768
+0.5273258
+4794
 
 
 Hospital B
-0.5429998
-5407
+0.5421512
+5504
 
 
 Hospital C
-0.5283993
-2324
+0.5394139
+2423
 
 
 Hospital D
-0.5222153
-3196
+0.5350195
+3084
 
 
 
@@ -1211,27 +1203,27 @@ Longest: 24

 
 
 Escherichia
-0.8230710
-0.9053398
-0.9872253
+0.8223045
+0.8921819
+0.9842872
 
 
 Klebsiella
-0.8203822
-0.9076433
-0.9847134
+0.8224414
+0.8927250
+0.9833539
 
 
 Staphylococcus
-0.8287654
-0.9192859
-0.9894393
+0.8268988
+0.9192531
+0.9861216
 
 
 Streptococcus
-0.5379310
+0.5447324
 0.0000000
-0.5379310
+0.5447324
 
 
 
diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png
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diff --git a/docs/articles/AMR_files/figure-html/plot 5-1.png b/docs/articles/AMR_files/figure-html/plot 5-1.png
index 1d36ff57..8d6a1c40 100644
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diff --git a/docs/articles/EUCAST.html b/docs/articles/EUCAST.html
index 83aad23a..ce5e1e90 100644
--- a/docs/articles/EUCAST.html
+++ b/docs/articles/EUCAST.html
@@ -39,7 +39,7 @@
       
       
         AMR (for R)
-        1.4.0.9046
+        1.5.0
diff --git a/docs/articles/MDR.html b/docs/articles/MDR.html index 5d6c140f..ac82c95a 100644 --- a/docs/articles/MDR.html +++ b/docs/articles/MDR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 @@ -311,19 +311,19 @@ Unique: 2

 head(my_TB_data)
 #   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin
-# 1          R         I            R          S            I            S
-# 2          I         S            I          S            S            R
-# 3          I         I            I          R            I            R
-# 4          S         S            I          S            R            I
-# 5          I         R            S          R            S            R
-# 6          I         I            I          R            S            I
+# 1          S         R            S          S            I            R
+# 2          R         I            S          I            S            I
+# 3          I         I            R          S            I            S
+# 4          R         S            R          I            R            S
+# 5          I         R            I          I            I            R
+# 6          I         R            I          R            S            R
 #   kanamycin
-# 1         S
+# 1         R
 # 2         I
 # 3         I
-# 4         S
-# 5         I
-# 6         R
+# 4 I +# 5 S +# 6 S

We can now add the interpretation of MDR-TB to our data set. You can use:

 mdro(my_TB_data, guideline = "TB")
@@ -354,40 +354,40 @@ Unique: 5

1 Mono-resistant -3219 -64.38% -3219 -64.38% +3286 +65.72% +3286 +65.72% 2 Negative -982 -19.64% -4201 -84.02% +992 +19.84% +4278 +85.56% 3 Multi-drug-resistant -434 -8.68% -4635 -92.70% +424 +8.48% +4702 +94.04% 4 Poly-resistant -251 -5.02% -4886 -97.72% +214 +4.28% +4916 +98.32% 5 Extensively drug-resistant -114 -2.28% +84 +1.68% 5000 100.00% diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index 4d16497f..83613b0a 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html index 8cfee5fe..a802f763 100644 --- a/docs/articles/SPSS.html +++ b/docs/articles/SPSS.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 @@ -193,7 +193,7 @@

How to import data from SPSS / SAS / Stata

Matthijs S. Berends

-

26 December 2020

+

29 December 2020

Source: vignettes/SPSS.Rmd diff --git a/docs/articles/WHONET.html b/docs/articles/WHONET.html index bdf56142..8073149b 100644 --- a/docs/articles/WHONET.html +++ b/docs/articles/WHONET.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 5d223b31..e7b6b63f 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 @@ -227,20 +227,34 @@ times = 10) print(S.aureus, unit = "ms", signif = 2) # Unit: milliseconds -# expr min lq mean median uq max neval -# as.mo("sau") 9.9 11 19.0 12.0 13.0 47.0 10 -# as.mo("stau") 100.0 110 130.0 130.0 140.0 150.0 10 -# as.mo("STAU") 110.0 110 130.0 140.0 140.0 150.0 10 -# as.mo("staaur") 11.0 11 15.0 12.0 13.0 40.0 10 -# as.mo("STAAUR") 12.0 12 21.0 13.0 40.0 46.0 10 -# as.mo("S. aureus") 26.0 31 45.0 34.0 60.0 86.0 10 -# as.mo("S aureus") 26.0 29 36.0 31.0 33.0 58.0 10 -# as.mo("Staphylococcus aureus") 1.6 2 2.3 2.3 2.7 2.8 10 -# as.mo("Staphylococcus aureus (MRSA)") 880.0 900 910.0 910.0 920.0 950.0 10 -# as.mo("Sthafilokkockus aaureuz") 370.0 370 380.0 380.0 380.0 400.0 10 -# as.mo("MRSA") 9.9 11 18.0 13.0 14.0 47.0 10 -# as.mo("VISA") 17.0 19 29.0 21.0 48.0 50.0 10 -# as.mo("VRSA") 16.0 19 29.0 20.0 47.0 55.0 10 +# expr min lq mean median uq max +# as.mo("sau") 13.0 14.0 25.0 15.0 44.0 65 +# as.mo("stau") 120.0 130.0 140.0 140.0 160.0 160 +# as.mo("STAU") 120.0 130.0 150.0 160.0 160.0 180 +# as.mo("staaur") 13.0 13.0 14.0 14.0 14.0 15 +# as.mo("STAAUR") 13.0 14.0 17.0 15.0 15.0 43 +# as.mo("S. aureus") 30.0 32.0 45.0 34.0 62.0 68 +# as.mo("S aureus") 31.0 34.0 42.0 35.0 61.0 63 +# as.mo("Staphylococcus aureus") 2.5 2.6 2.8 2.8 2.9 3 +# as.mo("Staphylococcus aureus (MRSA)") 1200.0 1200.0 1200.0 1200.0 1200.0 1200 +# as.mo("Sthafilokkockus aaureuz") 550.0 560.0 570.0 560.0 570.0 610 +# as.mo("MRSA") 13.0 13.0 17.0 15.0 15.0 42 +# as.mo("VISA") 21.0 22.0 26.0 23.0 23.0 52 +# as.mo("VRSA") 21.0 23.0 35.0 24.0 52.0 54 +# neval +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10 +# 10

In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.

To improve performance, two important calculations take almost no time at all: repetitive results and already precalculated results.

@@ -270,8 +284,8 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# mo_name(x) 136 169 210 198 247 317 10 -

So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.198 seconds. You only lose time on your unique input values.

+# mo_name(x) 141 180 218 207 245 312 10 +

So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.207 seconds. You only lose time on your unique input values.

@@ -285,10 +299,10 @@ print(run_it, unit = "ms", signif = 3) # Unit: milliseconds # expr min lq mean median uq max neval -# A 7.21 7.32 7.92 7.69 8.49 9.43 10 -# B 22.60 23.50 28.90 24.70 26.10 69.20 10 -# C 1.87 1.92 2.10 2.08 2.27 2.34 10

-

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0021 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

+# A 8.76 8.96 9.39 9.31 9.86 10.10 10 +# B 27.60 28.20 33.00 28.90 29.40 71.20 10 +# C 2.28 2.32 2.47 2.45 2.48 2.85 10 +

So going from mo_name("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0025 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

 run_it <- microbenchmark(A = mo_species("aureus"),
                          B = mo_genus("Staphylococcus"),
@@ -302,14 +316,14 @@
 print(run_it, unit = "ms", signif = 3)
 # Unit: milliseconds
 #  expr  min   lq mean median   uq  max neval
-#     A 1.34 1.59 1.66   1.65 1.74 2.18    10
-#     B 1.34 1.63 1.73   1.72 1.85 2.31    10
-#     C 1.41 1.61 1.65   1.65 1.72 1.83    10
-#     D 1.59 1.63 1.77   1.77 1.89 2.03    10
-#     E 1.33 1.60 1.68   1.65 1.73 2.08    10
-#     F 1.31 1.34 1.56   1.52 1.71 2.11    10
-#     G 1.34 1.60 1.75   1.64 1.76 2.74    10
-#     H 1.32 1.38 1.57   1.63 1.71 1.78    10
+# A 1.91 1.95 2.06 1.99 2.09 2.62 10 +# B 1.83 1.91 2.09 2.04 2.20 2.45 10 +# C 1.79 1.90 2.03 1.99 2.22 2.30 10 +# D 1.90 2.01 2.18 2.12 2.25 2.71 10 +# E 1.91 2.02 2.14 2.08 2.15 2.81 10 +# F 1.86 1.92 2.00 2.01 2.06 2.16 10 +# G 1.81 1.96 2.09 2.08 2.22 2.41 10 +# H 1.90 1.93 2.05 2.00 2.22 2.29 10

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.

@@ -337,13 +351,13 @@ print(run_it, unit = "ms", signif = 4) # Unit: milliseconds # expr min lq mean median uq max neval -# en 15.73 16.35 20.85 16.74 17.71 56.56 100 -# de 18.96 19.62 22.32 19.86 20.46 59.58 100 -# nl 31.06 31.91 37.31 32.78 34.57 75.58 100 -# es 18.92 19.59 23.43 19.92 20.42 62.72 100 -# it 18.80 19.36 22.59 19.74 20.54 62.72 100 -# fr 18.88 19.53 23.89 19.85 20.91 61.56 100 -# pt 18.89 19.51 21.46 19.87 20.29 59.12 100
+# en 17.45 18.01 19.69 18.53 19.14 55.30 100 +# de 20.58 21.54 26.69 22.08 23.96 67.16 100 +# nl 33.79 34.67 39.13 35.39 36.72 74.60 100 +# es 20.71 21.42 24.36 21.88 22.65 58.57 100 +# it 20.65 21.18 26.50 21.53 22.68 61.96 100 +# fr 20.68 21.27 25.05 21.64 22.37 58.82 100 +# pt 20.69 21.44 24.36 21.94 22.99 59.66 100

Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.

diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png index 19a9dea9..431f27bf 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index a8e6ad88..d2bddbd9 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/articles/index.html b/docs/articles/index.html index ee482346..2c8fb79f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/articles/resistance_predict.html b/docs/articles/resistance_predict.html index 79bf768c..e6b545a3 100644 --- a/docs/articles/resistance_predict.html +++ b/docs/articles/resistance_predict.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/articles/welcome_to_AMR.html b/docs/articles/welcome_to_AMR.html index 7e649944..40898fcb 100644 --- a/docs/articles/welcome_to_AMR.html +++ b/docs/articles/welcome_to_AMR.html @@ -39,7 +39,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/authors.html b/docs/authors.html index bcd08a4b..55f84d28 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/index.html b/docs/index.html index 513736a6..179b38c9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/news/index.html b/docs/news/index.html index 2c955b9f..f8c2edc2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 @@ -236,13 +236,13 @@ Source: NEWS.md -
-

-AMR 1.4.0.9052 Unreleased +
+

+AMR 1.4.0.9053 Unreleased

-
+

-Last updated: 28 December 2020 +Last updated: 29 December 2020

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 0c905352..bdfdf68e 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2020-12-28T21:24Z +last_built: 2020-12-29T20:22Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index b0a7f1ea..f4b3e940 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0

diff --git a/docs/reference/AMR.html b/docs/reference/AMR.html index c8496e0f..3cd74c81 100644 --- a/docs/reference/AMR.html +++ b/docs/reference/AMR.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0
diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index 74ba73e9..0c1b2326 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0
diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 54233c88..a0fbb456 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0
diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html index 3e66899a..92c2e880 100644 --- a/docs/reference/ab_from_text.html +++ b/docs/reference/ab_from_text.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.4.0.9053

@@ -285,7 +285,7 @@

A list, or a character if collapse is not NULL

Details

-

This function is also internally used by as.ab(), although it then only searches for the first drug name and will throw a note if more drug names could have been returned.

Argument type

+

This function is also internally used by as.ab(), although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the as.ab() function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.

Argument type

At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses as.ab() internally, it will correct for misspelling.

diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index 51c5c6d6..c3df214b 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/age.html b/docs/reference/age.html index 6705c9ab..cf72930e 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index 1a277aeb..65f7daff 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index c97bd1a6..72791542 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9051 + 1.5.0 diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 81f79ab4..6c60e9e8 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 2af88481..3181dbd9 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index cf0f59c6..1bc1e5fa 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index d5260a2e..a66a2c08 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index becd1295..f562904d 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 55e2cc3f..c678db22 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index 3281db16..89994ec7 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/availability.html b/docs/reference/availability.html index af2e53a7..fda075da 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index 799d2f78..3f31ab6f 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index f3e3bc1c..139f7576 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index b35010b7..97c6fcfe 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/count.html b/docs/reference/count.html index 564fe975..d12114b8 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 19dc97f5..dd498d35 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.4.0.9052 + 1.5.0 @@ -289,7 +289,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied ampc_cephalosporin_resistance -

a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to NA. Currently only works when version_expertrules is 3.2; 'EUCAST Expert Rules v3.2 on Enterobacterales' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of NA for this argument will remove results for these agents, while e.g. a value of "R" will make the results for these agents resistant. Use NULL to not alter the results for AmpC de-repressed cephalosporin-resistant mutants.
For EUCAST Expert Rules v3.2, this rule applies to: Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia.

+

a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to NA. Currently only works when version_expertrules is 3.2; 'EUCAST Expert Rules v3.2 on Enterobacterales' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of NA for this argument will remove results for these agents, while e.g. a value of "R" will make the results for these agents resistant. Use NULL to not alter the results for AmpC de-repressed cephalosporin-resistant mutants.
For EUCAST Expert Rules v3.2, this rule applies to: Enterobacter, Klebsiella aerogenes, Citrobacter braakii, freundii, gillenii, murliniae, rodenticum, sedlakii, werkmanii, youngae, Hafnia alvei, Serratia, Morganella morganii, Providencia.

... diff --git a/docs/reference/example_isolates.html b/docs/reference/example_isolates.html index 70b373bb..df9289b6 100644 --- a/docs/reference/example_isolates.html +++ b/docs/reference/example_isolates.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/example_isolates_unclean.html b/docs/reference/example_isolates_unclean.html index fb89c297..5bacd5e9 100644 --- a/docs/reference/example_isolates_unclean.html +++ b/docs/reference/example_isolates_unclean.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index d0bc8f15..4175bf3d 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9051 + 1.5.0 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index e1dc82be..f66c3d98 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index ae075c6e..bf77d494 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index f780af55..30cfb64c 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 0d086ee2..c1d9d974 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index c30a6bd4..d279f4d8 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index b13893b7..c020ca26 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ccbdb49..74170f49 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/docs/reference/intrinsic_resistant.html b/docs/reference/intrinsic_resistant.html index 6b9b6723..8e4efe2b 100644 --- a/docs/reference/intrinsic_resistant.html +++ b/docs/reference/intrinsic_resistant.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/join.html b/docs/reference/join.html index e70d453d..d2bb0dd4 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/key_antibiotics.html b/docs/reference/key_antibiotics.html index 6e95e09b..4daf9c01 100644 --- a/docs/reference/key_antibiotics.html +++ b/docs/reference/key_antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index f9dacfb5..18a5cd9f 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index 7b22cef1..3de9ec5d 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/like.html b/docs/reference/like.html index 31a8a7cf..fc00ba0e 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 0bd0d11a..8c40d303 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 033c8fbd..aa86be6e 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 100f9da6..00a18265 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 9b64ce45..0ea63b27 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index 6578ef4d..3cd1361d 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 766dda35..253f3d4f 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index ea585b5b..a924a632 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 08f03885..1a517f90 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 65478bdd..a462e4e3 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index da4aa2f9..2fd9dbcc 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/random.html b/docs/reference/random.html index 8fe8fa3e..5ee97d67 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 637bfe71..e6a2f9cc 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9050 + 1.5.0 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index bcfe6e26..88e33ad2 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index c4d5ab8a..60bbe35c 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index fcd33ebe..f195c4e9 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9046 + 1.5.0 diff --git a/docs/survey.html b/docs/survey.html index 67690079..246cad47 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9052 + 1.4.0.9053 diff --git a/git_premaster.sh b/git_premaster.sh index e44d92a5..49921590 100755 --- a/git_premaster.sh +++ b/git_premaster.sh @@ -120,13 +120,21 @@ echo "• Updating internal data •" echo "••••••••••••••••••••••••••" Rscript -e "source('data-raw/internals.R')" echo +echo "••••••••••••••••••••" +echo "• Building package •" +echo "••••••••••••••••••••" +echo "• Removing old build..." +rm data-raw/AMR_*.tar.gz +echo "• Building to 'data-raw'..." +Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)" +echo "• Installing..." +Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)" +echo echo "•••••••••••••••••" echo "• Building site •" echo "•••••••••••••••••" -echo "• Installing..." -Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)" Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))" -# add the survey +# add the survey page Rscript -e "source('data-raw/create_survey_page.R')" echo echo "•••••••••••••••••••••••••" @@ -148,7 +156,7 @@ echo "•••••••••••••••••••••••• # save latest changes as well git add . # and commit -git commit -a -m "(v$new_version) $1" --quiet +git commit -a -m "(v${new_version}) $1" --quiet git push --quiet echo "Comparison:" echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline" diff --git a/man/ab_from_text.Rd b/man/ab_from_text.Rd index 16dbdfc6..f5431f7f 100644 --- a/man/ab_from_text.Rd +++ b/man/ab_from_text.Rd @@ -33,7 +33,7 @@ A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL} Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts. } \details{ -This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. +This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. \subsection{Argument \code{type}}{ At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling. diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 852671b3..110f3f10 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -42,7 +42,7 @@ eucast_rules( \item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.} -\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter, Klebsiella aerogenes, Citrobacter freundii, Hafnia alvei, Serratia, Morganella morganii, Providencia}.} +\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter, Klebsiella aerogenes, Citrobacter braakii, freundii, gillenii, murliniae, rodenticum, sedlakii, werkmanii, youngae, Hafnia alvei, Serratia, Morganella morganii, Providencia}.} \item{...}{column name of an antibiotic, please see section \emph{Antibiotics} below} } diff --git a/tests/testthat.R b/tests/testthat.R index e7489675..09c15c2b 100755 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -23,7 +23,11 @@ # how to conduct AMR analysis: https://msberends.github.io/AMR/ # # ==================================================================== # -library(testthat, warn.conflicts = FALSE) -library(AMR) - -test_check("AMR") +if (require("testthat")) { + # the testthat package is in Suggests, but very old R versions will not be + # able to install it. Yet, we want checks in those R versions as well, so + # only run unit tests in later R versions: + library(testthat, warn.conflicts = FALSE) + library(AMR) + test_check("AMR") +}