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(v1.2.0.9038) CLSI 2019 fix

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  1. 4
      .github/workflows/check.yaml
  2. 4
      DESCRIPTION
  3. 5
      NEWS.md
  4. 14
      R/aa_helper_functions.R
  5. 2
      R/rsi.R
  6. 23
      data-raw/reproduction_of_rsi_translation.R
  7. 542
      data-raw/rsi_translation.txt
  8. BIN
      data/rsi_translation.rda
  9. 2
      docs/404.html
  10. 2
      docs/LICENSE-text.html
  11. 4
      docs/articles/PCA.html
  12. 2
      docs/articles/index.html
  13. 2
      docs/authors.html
  14. 2
      docs/index.html
  15. 13
      docs/news/index.html
  16. 2
      docs/pkgdown.yml
  17. 2
      docs/reference/AMR-deprecated.html
  18. 2
      docs/reference/AMR.html
  19. 2
      docs/reference/WHOCC.html
  20. 2
      docs/reference/WHONET.html
  21. 2
      docs/reference/ab_from_text.html
  22. 2
      docs/reference/ab_property.html
  23. 2
      docs/reference/age.html
  24. 2
      docs/reference/age_groups.html
  25. 2
      docs/reference/antibiotics.html
  26. 2
      docs/reference/as.ab.html
  27. 2
      docs/reference/as.disk.html
  28. 2
      docs/reference/as.mic.html
  29. 2
      docs/reference/as.mo.html
  30. 4
      docs/reference/as.rsi.html
  31. 2
      docs/reference/atc_online.html
  32. 2
      docs/reference/availability.html
  33. 2
      docs/reference/bug_drug_combinations.html
  34. 2
      docs/reference/catalogue_of_life.html
  35. 2
      docs/reference/catalogue_of_life_version.html
  36. 2
      docs/reference/count.html
  37. 2
      docs/reference/eucast_rules.html
  38. 2
      docs/reference/example_isolates.html
  39. 2
      docs/reference/example_isolates_unclean.html
  40. 2
      docs/reference/filter_ab_class.html
  41. 2
      docs/reference/first_isolate.html
  42. 2
      docs/reference/g.test.html
  43. 2
      docs/reference/ggplot_pca.html
  44. 2
      docs/reference/ggplot_rsi.html
  45. 2
      docs/reference/guess_ab_col.html
  46. 2
      docs/reference/index.html
  47. 2
      docs/reference/join.html
  48. 2
      docs/reference/key_antibiotics.html
  49. 2
      docs/reference/kurtosis.html
  50. 2
      docs/reference/like.html
  51. 2
      docs/reference/mdro.html
  52. 2
      docs/reference/microorganisms.codes.html
  53. 2
      docs/reference/microorganisms.html
  54. 2
      docs/reference/microorganisms.old.html
  55. 2
      docs/reference/mo_property.html
  56. 2
      docs/reference/mo_source.html
  57. 2
      docs/reference/p_symbol.html
  58. 2
      docs/reference/proportion.html
  59. 2
      docs/reference/resistance_predict.html
  60. 4
      docs/reference/rsi_translation.html
  61. 2
      docs/reference/skewness.html
  62. 2
      docs/reference/translate.html
  63. 2
      docs/survey.html
  64. 2
      man/as.rsi.Rd
  65. 2
      man/rsi_translation.Rd

4
.github/workflows/check.yaml

@ -48,7 +48,7 @@ jobs: @@ -48,7 +48,7 @@ jobs:
# - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: windows-latest, r: 'devel'}
- {os: macOS-latest, r: 'devel'}
# - {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: windows-latest, r: '3.6'}
# - {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# - {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@ -118,7 +118,7 @@ jobs: @@ -118,7 +118,7 @@ jobs:
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
uses: actions/upload-artifact@main
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check

4
DESCRIPTION

@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 1.2.0.9037
Date: 2020-07-28
Version: 1.2.0.9038
Date: 2020-07-29
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

5
NEWS.md

@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
# AMR 1.2.0.9037
## <small>Last updated: 28 July 2020</small>
# AMR 1.2.0.9038
## <small>Last updated: 29 July 2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@ -32,6 +32,7 @@ @@ -32,6 +32,7 @@
* Fixed a bug where `as.ab()` would return an error on invalid input values
* The `as.ab()` function will now throw a note if more than 1 antimicrobial drug could be retrieved from a single input value.
* Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded
* Fixed a bug for CLSI 2019 guidelines (using `as.rsi()`), that also included results for animals. It now only contains interpretation guidelines for humans.
* All `*_join_microorganisms()` functions and `bug_drug_combinations()` now return the original data class (e.g. `tibble`s and `data.table`s)
* For functions `rsi_df()`, `proportion_df()` and `count_df()`:
* Fixed a bug for using grouped versions

14
R/aa_helper_functions.R

@ -419,13 +419,7 @@ font_stripstyle <- function(x) { @@ -419,13 +419,7 @@ font_stripstyle <- function(x) {
}
progress_estimated <- function(n = 1, n_min = 0, ...) {
if (n >= n_min & interactive()) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
}
pb
} else {
if (!interactive() || n < n_min) {
pb <- list()
pb$tick <- function() {
invisible()
@ -434,6 +428,12 @@ progress_estimated <- function(n = 1, n_min = 0, ...) { @@ -434,6 +428,12 @@ progress_estimated <- function(n = 1, n_min = 0, ...) {
invisible()
}
structure(pb, class = "txtProgressBar")
} else if (n >= n_min) {
pb <- utils::txtProgressBar(max = n, style = 3)
pb$tick <- function() {
pb$up(pb$getVal() + 1)
}
pb
}
}

2
R/rsi.R

@ -37,7 +37,7 @@ @@ -37,7 +37,7 @@
#'
#' Supported guidelines to be used as input for the `guideline` parameter are: `r paste0('"', sort(unique(AMR::rsi_translation$guideline)), '"', collapse = ", ")`. Simply using `"CLSI"` or `"EUCAST"` for input will automatically select the latest version of that guideline.
#'
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**.
#' The repository of this package [contains a machine readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#'
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'

23
data-raw/reproduction_of_rsi_translation.R

@ -1,12 +1,19 @@ @@ -1,12 +1,19 @@
library(dplyr)
library(readr)
library(tidyr)
# Installed WHONET 2019 software on Windows (http://www.whonet.org/software.html),
# opened C:\WHONET\Codes\WHONETCodes.mdb in MS Access
# and exported table 'DRGLST1' to MS Excel
DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx", na = c("", "NA", "-"))
rsi_translation <- DRGLST1 %>%
rsi_trans <- DRGLST1 %>%
# only keep CLSI and EUCAST guidelines:
filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
filter(GUIDELINES %like% "^(CLSI|EUCST)")
if (any(is.na(rsi_trans$BREAKPOINT_TYPE)) | !"Human" %in% rsi_trans$BREAKPOINT_TYPE) {
stop("Check column BREAKPOINT_TYPE - something is WRONG!")
}
rsi_trans <- rsi_trans %>%
filter(BREAKPOINT_TYPE == "Human") %>%
mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
# set a nice layout:
@ -29,15 +36,15 @@ rsi_translation <- DRGLST1 %>% @@ -29,15 +36,15 @@ rsi_translation <- DRGLST1 %>%
print(mo_failures())
# create 2 tables: MIC and disk
tbl_mic <- rsi_translation %>%
tbl_mic <- rsi_trans %>%
filter(method == "MIC") %>%
mutate(breakpoint_S = as.double(S_mic), breakpoint_R = as.double(R_mic))
tbl_disk <- rsi_translation %>%
tbl_disk <- rsi_trans %>%
filter(method == "DISK") %>%
mutate(breakpoint_S = as.double(S_disk), breakpoint_R = as.double(R_disk))
# merge them so every record is a unique combination of method, mo and ab
rsi_translation <- bind_rows(tbl_mic, tbl_disk) %>%
rsi_trans <- bind_rows(tbl_mic, tbl_disk) %>%
rename(disk_dose = dose_disk) %>%
mutate(disk_dose = gsub("µ", "u", disk_dose)) %>%
select(-ends_with("_mic"), -ends_with("_disk"))
@ -70,8 +77,8 @@ clsi_general <- read_tsv("data-raw/DRGLST.txt") %>% @@ -70,8 +77,8 @@ clsi_general <- read_tsv("data-raw/DRGLST.txt") %>%
# add new EUCAST with read_EUCAST.R
# 2020-04-14 did that now for 2019 and 2020
rsi_translation <- rsi_translation %>%
# filter(guideline != "EUCAST 2019") %>%
rsi_trans <- rsi_trans %>%
filter(guideline != "EUCAST 2019") %>%
bind_rows(new_EUCAST) %>%
bind_rows(clsi_general) %>%
mutate(uti = site %like% "(UTI|urinary)") %>%
@ -82,6 +89,8 @@ rsi_translation <- rsi_translation %>% @@ -82,6 +89,8 @@ rsi_translation <- rsi_translation %>%
arrange(desc(guideline), ab, mo, method)
# save to package
rsi_translation <- rsi_trans
usethis::use_data(rsi_translation, overwrite = TRUE)
rm(rsi_trans)
rm(rsi_translation)
devtools::load_all(".")

542
data-raw/rsi_translation.txt

File diff suppressed because it is too large Load Diff

BIN
data/rsi_translation.rda

Binary file not shown.

2
docs/404.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/LICENSE-text.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

4
docs/articles/PCA.html

@ -39,7 +39,7 @@ @@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>
@ -186,7 +186,7 @@ @@ -186,7 +186,7 @@
<h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">24 July 2020</h4>
<h4 class="date">29 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
<div class="hidden name"><code>PCA.Rmd</code></div>

2
docs/articles/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/authors.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/index.html

@ -43,7 +43,7 @@ @@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

13
docs/news/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>
@ -229,13 +229,13 @@ @@ -229,13 +229,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1209037" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9037">
<a href="#amr-1209037" class="anchor"></a>AMR 1.2.0.9037<small> Unreleased </small>
<div id="amr-1209038" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9038">
<a href="#amr-1209038" class="anchor"></a>AMR 1.2.0.9038<small> Unreleased </small>
</h1>
<div id="last-updated-28-july-2020" class="section level2">
<div id="last-updated-29-july-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-28-july-2020" class="anchor"></a><small>Last updated: 28 July 2020</small>
<a href="#last-updated-29-july-2020" class="anchor"></a><small>Last updated: 29 July 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -284,6 +284,7 @@ @@ -284,6 +284,7 @@
</ul>
</li>
<li><p>Fixed a bug where <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> would not work on a tibble when the <code>tibble</code> or <code>dplyr</code> package was loaded</p></li>
<li><p>Fixed a bug for CLSI 2019 guidelines (using <code><a href="../reference/as.rsi.html">as.rsi()</a></code>), that also included results for animals. It now only contains interpretation guidelines for humans.</p></li>
<li><p>All <code>*_join_microorganisms()</code> functions and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> now return the original data class (e.g. <code>tibble</code>s and <code>data.table</code>s)</p></li>
<li>
<p>For functions <code><a href="../reference/proportion.html">rsi_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code> and <code><a href="../reference/count.html">count_df()</a></code>:</p>

2
docs/pkgdown.yml

@ -10,7 +10,7 @@ articles: @@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html
benchmarks: benchmarks.html
resistance_predict: resistance_predict.html
last_built: 2020-07-28T16:39Z
last_built: 2020-07-29T08:31Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles

2
docs/reference/AMR-deprecated.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/AMR.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/WHOCC.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/WHONET.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/ab_from_text.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/ab_property.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/age.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/age_groups.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/antibiotics.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/as.ab.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/as.disk.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/as.mic.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/as.mo.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

4
docs/reference/as.rsi.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>
@ -308,7 +308,7 @@ @@ -308,7 +308,7 @@
<p>When using <code>as.rsi()</code> on untransformed data, the data will be cleaned to only contain values S, I and R. When using the function on data with class <code><a href='as.mic.html'>mic</a></code> (using <code><a href='as.mic.html'>as.mic()</a></code>) or class <code><a href='as.disk.html'>disk</a></code> (using <code><a href='as.disk.html'>as.disk()</a></code>), the data will be interpreted based on the guideline set with the <code>guideline</code> parameter.</p>
<p>Supported guidelines to be used as input for the <code>guideline</code> parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> for input will automatically select the latest version of that guideline.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>.</p>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine readable version</a> of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>

2
docs/reference/atc_online.html

@ -83,7 +83,7 @@ This function requires an internet connection." /> @@ -83,7 +83,7 @@ This function requires an internet connection." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/availability.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/bug_drug_combinations.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/catalogue_of_life_version.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/count.html

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( @@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/eucast_rules.html

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied @@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/example_isolates.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/example_isolates_unclean.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/filter_ab_class.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/first_isolate.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/g.test.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/ggplot_pca.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/guess_ab_col.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/index.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/join.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/key_antibiotics.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/kurtosis.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/like.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/mdro.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/microorganisms.codes.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/microorganisms.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/microorganisms.old.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/mo_property.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/mo_source.html

@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p @@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/p_symbol.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/proportion.html

@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be @@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/resistance_predict.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

4
docs/reference/rsi_translation.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>
@ -240,7 +240,7 @@ @@ -240,7 +240,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 18,964 observations and 10 variables:</p><ul>
<p>A <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with 18,650 observations and 10 variables:</p><ul>
<li><p><code>guideline</code><br /> Name of the guideline</p></li>
<li><p><code>method</code><br /> Either "MIC" or "DISK"</p></li>
<li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li>

2
docs/reference/skewness.html

@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr @@ -83,7 +83,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/reference/translate.html

@ -82,7 +82,7 @@ @@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
docs/survey.html

@ -81,7 +81,7 @@ @@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9038</span>
</span>
</div>

2
man/as.rsi.Rd

@ -64,7 +64,7 @@ When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will @@ -64,7 +64,7 @@ When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will
Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline.
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}.
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.

2
man/rsi_translation.Rd

@ -5,7 +5,7 @@ @@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data set for R/SI interpretation}
\format{
A \code{\link{data.frame}} with 18,964 observations and 10 variables:
A \code{\link{data.frame}} with 18,650 observations and 10 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "MIC" or "DISK"

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