diff --git a/DESCRIPTION b/DESCRIPTION index ff75d4e8..86e3b5d9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.6.0.9013 -Date: 2021-04-29 +Version: 1.6.0.9014 +Date: 2021-04-30 Title: Antimicrobial Resistance Data Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 2b7dbd19..fc558bef 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.6.0.9013 -## Last updated: 29 April 2021 +# `AMR` 1.6.0.9014 +## Last updated: 30 April 2021 ### New * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()` @@ -31,9 +31,11 @@ * Fixed an installation error on R-3.0 * Added `info` argument to `as.mo()` to turn on/off the progress bar * Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error +* Fix for transforming numeric values to RSI (`as.rsi()`) when the `vctrs` package is loaded (i.e., when using tidyverse) +* Colour fix for using `barplot()` on an RSI class -# AMR 1.6.0 +# `AMR` 1.6.0 ### New * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package. @@ -127,7 +129,7 @@ * Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB) -# AMR 1.5.0 +# `AMR` 1.5.0 ### 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()`): @@ -204,7 +206,7 @@ * Added CodeFactor as a continuous code review to this package: * Added Dr. Rogier Schade as contributor -# AMR 1.4.0 +# `AMR` 1.4.0 ### New * Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`. @@ -276,7 +278,7 @@ * Removed unnecessary references to the `base` package * Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file -# AMR 1.3.0 +# `AMR` 1.3.0 ### 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 @@ -329,7 +331,7 @@ ### Other * Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI. -# AMR 1.2.0 +# `AMR` 1.2.0 ### Breaking * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users. @@ -367,7 +369,7 @@ * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()` * Removed function `read.4d()`, that was only useful for reading data from an old test database. -# AMR 1.1.0 +# `AMR` 1.1.0 ### New * Support for easy principal component analysis for AMR, using the new `pca()` function @@ -389,7 +391,7 @@ * Support for the upcoming `dplyr` version 1.0.0 * More robust assigning for classes `rsi` and `mic` -# AMR 1.0.1 +# `AMR` 1.0.1 ### Changed * Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline @@ -405,7 +407,7 @@ * Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs * Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown) -# AMR 1.0.0 +# `AMR` 1.0.0 This software is now out of beta and considered stable. Nonetheless, this package will be developed continually. @@ -453,7 +455,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag * Full support for the upcoming R 4.0 * Removed unnecessary `AMR::` calls -# AMR 0.9.0 +# `AMR` 0.9.0 ### Breaking * Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family. @@ -519,7 +521,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request * Added Dr. Sofia Ny as contributor -# AMR 0.8.0 +# `AMR` 0.8.0 ### Breaking * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`: @@ -648,7 +650,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag * Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors * Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package -# AMR 0.7.1 +# `AMR` 0.7.1 #### New * Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates: @@ -709,7 +711,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag #### Other * Fixed a note thrown by CRAN tests -# AMR 0.7.0 +# `AMR` 0.7.0 #### New * Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values. @@ -767,13 +769,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag #### Other * Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html) -# AMR 0.6.1 +# `AMR` 0.6.1 #### Changed * Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE` * Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy -# AMR 0.6.0 +# `AMR` 0.6.0 **New website!** @@ -966,7 +968,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git #### Other * Updated licence text to emphasise GPL 2.0 and that this is an R package. -# AMR 0.5.0 +# `AMR` 0.5.0 #### New * Repository moved to GitLab @@ -1049,7 +1051,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git * Updated vignettes to comply with README -# AMR 0.4.0 +# `AMR` 0.4.0 #### New * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms. @@ -1160,7 +1162,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git #### Other * More unit tests to ensure better integrity of functions -# AMR 0.3.0 +# `AMR` 0.3.0 #### New * **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated. @@ -1230,7 +1232,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git * Windows: https://ci.appveyor.com/project/msberends/amr * Added thesis advisors to DESCRIPTION file -# AMR 0.2.0 +# `AMR` 0.2.0 #### New * Full support for Windows, Linux and macOS @@ -1265,7 +1267,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git * Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR) * Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R) -# AMR 0.1.1 +# `AMR` 0.1.1 * `EUCAST_rules` applies for amoxicillin even if ampicillin is missing * Edited column names to comply with GLIMS, the laboratory information system @@ -1273,6 +1275,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git * Renamed 'Daily Defined Dose' to 'Defined Daily Dose' * Added barplots for `rsi` and `mic` classes -# AMR 0.1.0 +# `AMR` 0.1.0 * First submission to CRAN. diff --git a/R/plot.R b/R/plot.R index 75940a66..40fd7c48 100644 --- a/R/plot.R +++ b/R/plot.R @@ -586,6 +586,8 @@ barplot.rsi <- function(height, if (length(colours_RSI) == 1) { colours_RSI <- rep(colours_RSI, 3) + } else { + colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1]) } main <- gsub(" +", " ", paste0(main, collapse = " ")) diff --git a/R/rsi.R b/R/rsi.R index e4eba008..ab57ca14 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -259,9 +259,10 @@ as.rsi.default <- function(x, ...) { } if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) { - x[x == 1] <- "S" - x[x == 2] <- "I" - x[x == 3] <- "R" + x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error + x[x == "1"] <- "S" + x[x == "2"] <- "I" + x[x == "3"] <- "R" } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) { diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 94f912ea..9edabfab 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 75a4c03f..57f35341 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e992ea0c..f2a4ca14 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 diff --git a/docs/articles/index.html b/docs/articles/index.html index c2d27b84..b1cc2633 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 diff --git a/docs/authors.html b/docs/authors.html index e0b76a1b..45c34b8b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 diff --git a/docs/extra.js b/docs/extra.js index 4becd642..d2e8ae8d 100644 --- a/docs/extra.js +++ b/docs/extra.js @@ -39,14 +39,19 @@ $(document).ready(function() { if (url_old != url_new) { window.location.replace(url_new); } + + // Edit title of manual + $('.template-reference-index h1').text('Manual'); // replace 'Value' in manual with 'Returned value' $(".template-reference-topic h2#value").text("Returned value"); // replace \donttest and \dontrun texts in Examples - $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); - $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); - $("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); + if ($("pre.examples").length > 0) { + $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); + $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); + $("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); + } // PR for 'R for Data Science' on How To pages if ($(".template-article").length > 0) { @@ -106,9 +111,6 @@ $(document).ready(function() { $('.template-citation-authors h1').eq(1).html("All contributors of the AMR package"); $(".developers").html(doct_tit($(".developers").html())); $(".developers a[href='authors.html']").text("All contributors..."); - - // Edit title of manual - $('.template-reference-index h1').text('Manual'); }); $('head').append(" "); diff --git a/docs/index.html b/docs/index.html index b70546f6..07370872 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 diff --git a/docs/news/index.html b/docs/news/index.html index ab45b867..b37936f3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014 @@ -236,13 +236,12 @@ Source: NEWS.md -
-

-AMR 1.6.0.9013 Unreleased -

-
+
+

+ Unreleased AMR 1.6.0.9014

+

-Last updated: 29 April 2021 +Last updated: 30 April 2021

@@ -296,14 +295,15 @@
  • Fixed an installation error on R-3.0
  • Added info argument to as.mo() to turn on/off the progress bar
  • Fixed a bug that col_mo for some functions (esp. eucast_rules() and mdro()) could not be column names of the microorganisms data set as it would throw an error
    • +
  • Fix for transforming numeric values to RSI (as.rsi()) when the vctrs package is loaded (i.e., when using tidyverse)
    • +
  • Colour fix for using barplot() on an RSI class

    • -AMR 1.6.0 2021-03-14 -

    + 2021-03-14 AMR 1.6.0

    New

    @@ -339,7 +339,7 @@ #> Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"

  • Support for custom MDRO guidelines, using the new custom_mdro_guideline() function, please see mdro() for additional info

    • -

  • ggplot() generics for classes <mic> and <disk>

    • +

  • ggplot() generics for classes <mic> and <disk>

  • Function mo_is_yeast(), which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:

    @@ -396,7 +396,7 @@
 
  • Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent
    • 
 
  • All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
    • 
 
  • Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see translate)
    • 
-
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    • 
+
  • Plotting is now possible with base R using plot() and with ggplot2 using ggplot() on any vector of MIC and disk diffusion values
    •
  • Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the microorganisms data set
    • @@ -440,8 +440,7 @@

    -AMR 1.5.0 2021-01-06 -

    + 2021-01-06 AMR 1.5.0

    New

    @@ -554,8 +553,7 @@

    -AMR 1.4.0 2020-10-08 -

    + 2020-10-08 AMR 1.4.0

    New

    @@ -658,8 +656,7 @@

    -AMR 1.3.0 2020-07-31 -

    + 2020-07-31 AMR 1.3.0

    New

    @@ -741,8 +738,7 @@

    -AMR 1.2.0 2020-05-28 -

    + 2020-05-28 AMR 1.2.0

    Breaking

    @@ -805,8 +801,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 1.1.0 2020-04-15 -

    + 2020-04-15 AMR 1.1.0

    New

    @@ -847,8 +842,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 1.0.1 2020-02-23 -

    + 2020-02-23 AMR 1.0.1

    Changed

    @@ -872,8 +866,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 1.0.0 2020-02-17 -

    + 2020-02-17 AMR 1.0.0

    This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.

    @@ -951,8 +944,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.9.0 2019-11-29 -

    + 2019-11-29 AMR 0.9.0

    Breaking

    @@ -1059,8 +1051,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.8.0 2019-10-15 -

    + 2019-10-15 AMR 0.8.0

    Breaking

    @@ -1225,8 +1216,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.7.1 2019-06-23 -

    + 2019-06-23 AMR 0.7.1

    New

    @@ -1310,8 +1300,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.7.0 2019-06-03 -

    + 2019-06-03 AMR 0.7.0

    New

    @@ -1407,8 +1396,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.6.1 2019-03-29 -

    + 2019-03-29 AMR 0.6.1

    Changed

    @@ -1421,8 +1409,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.6.0 2019-03-27 -

    + 2019-03-27 AMR 0.6.0

    New website!

    We’ve got a new website: https://msberends.gitlab.io/AMR (built with the great pkgdown)

      @@ -1673,8 +1660,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.5.0 2018-11-30 -

    + 2018-11-30 AMR 0.5.0

    New

    @@ -1797,8 +1783,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.4.0 2018-10-01 -

    + 2018-10-01 AMR 0.4.0

    New

    @@ -1946,8 +1931,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.3.0 2018-08-14 -

    + 2018-08-14 AMR 0.3.0

    New

    @@ -2083,8 +2067,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.2.0 2018-05-03 -

    + 2018-05-03 AMR 0.2.0

    New

    @@ -2141,8 +2124,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.1.1 2018-03-14 -

    + 2018-03-14 AMR 0.1.1
    • EUCAST_rules applies for amoxicillin even if ampicillin is missing
      • @@ -2154,8 +2136,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

    -AMR 0.1.0 2018-02-22 -

    + 2018-02-22 AMR 0.1.0
    • First submission to CRAN.
    diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 331603a4..9a7641f7 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: 2021-04-29T15:15Z +last_built: 2021-04-30T08:14Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 240f6da1..b97f6bff 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014
    diff --git a/docs/survey.html b/docs/survey.html index 568d7cd0..10a6a0c9 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9013 + 1.6.0.9014
    diff --git a/git_premaster.sh b/git_premaster.sh index 00373e82..4393cebc 100755 --- a/git_premaster.sh +++ b/git_premaster.sh @@ -99,7 +99,7 @@ else fi # set version number to DESCRIPTION and NEWS files sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION -sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md +sed -i -- "1s/.*/# \`AMR\` ${new_version}/" NEWS.md rm *-- || true echo "• First 3 lines of DESCRIPTION:" head -3 DESCRIPTION diff --git a/pkgdown/extra.js b/pkgdown/extra.js index 4becd642..d2e8ae8d 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -39,14 +39,19 @@ $(document).ready(function() { if (url_old != url_new) { window.location.replace(url_new); } + + // Edit title of manual + $('.template-reference-index h1').text('Manual'); // replace 'Value' in manual with 'Returned value' $(".template-reference-topic h2#value").text("Returned value"); // replace \donttest and \dontrun texts in Examples - $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); - $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); - $("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); + if ($("pre.examples").length > 0) { + $("pre.examples").html($("pre.examples").html().replaceAll("# \\donttest{", "")); + $("pre.examples").html($("pre.examples").html().replaceAll("# \\dontrun{", "")); + $("pre.examples").html($("pre.examples").html().replaceAll("# }", "")); + } // PR for 'R for Data Science' on How To pages if ($(".template-article").length > 0) { @@ -106,9 +111,6 @@ $(document).ready(function() { $('.template-citation-authors h1').eq(1).html("All contributors of the AMR package"); $(".developers").html(doct_tit($(".developers").html())); $(".developers a[href='authors.html']").text("All contributors..."); - - // Edit title of manual - $('.template-reference-index h1').text('Manual'); }); $('head').append(" "); diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 1ac64eb3..5cd6aca0 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -175,7 +175,7 @@ test_that("first isolates work", { # shortcuts expect_identical(filter_first_isolate(example_isolates), - subset(example_isolates, first_isolate(example_isolates, method = "episode-based"))) + subset(example_isolates, first_isolate(example_isolates))) # notice that all mo's are distinct, so all are TRUE