diff --git a/DESCRIPTION b/DESCRIPTION index 248673ffc..10f57b28d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.8.0.9003 -Date: 2022-03-02 +Version: 1.8.0.9004 +Date: 2022-03-03 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index a2efa9ccb..6c57d18bf 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.8.0.9003 -## Last updated: 2 March 2022 +# `AMR` 1.8.0.9004 +## Last updated: 3 March 2022 All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months. @@ -11,6 +11,8 @@ All functions in this package are considered to be stable. Updates to the AMR in #> [1] "Staphylococcus aureus" ``` * More informative warning messages +* Added 192 as valid MIC +* Updated MIC printing in tibbles ### Other * Fix for unit testing on R 3.3 diff --git a/R/mic.R b/R/mic.R index f516dc81a..e9bb97e6a 100755 --- a/R/mic.R +++ b/R/mic.R @@ -37,8 +37,8 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops, function(x) paste0(x, sort(c(1:9, 1.5)))))), c(t(vapply(FUN.VALUE = character(45), ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))), - c(t(vapply(FUN.VALUE = character(16), ops, - function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12)))))))) + c(t(vapply(FUN.VALUE = character(17), ops, + function(x) paste0(x, sort(c(2 ^ c(7:11), 192, 80 * c(2:12)))))))) #' Transform Input to Minimum Inhibitory Concentrations (MIC) #' @@ -247,7 +247,9 @@ pillar_shaft.mic <- function(x, ...) { out <- pasted out[is.na(x)] <- font_na(NA) out <- gsub("(<|=|>)", font_silver("\\1"), out) - out <- gsub("([.]?0+)$", font_white("\\1"), out) + if (any(out %like% "[.]", na.rm = TRUE)) { + out <- gsub("([.]?0+)$", font_white("\\1"), out) + } create_pillar_column(out, align = "right", width = max(nchar(pasted))) } diff --git a/R/rsi.R b/R/rsi.R index fc6fa2cc4..33c9215a4 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -67,7 +67,7 @@ #' #' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`). #' -#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored. +#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(rsi_translation, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(rsi_translation, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored. #' #' ## After Interpretation #' diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index e360c650c..a5d13f578 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 f5af4f337..88793f5fc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -43,7 +43,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 06936e3a6..6a5c4d38c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index a7832a2f0..96ba838f2 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004 @@ -185,12 +185,12 @@ -
+

Data sets for download / own use

-

02 March 2022

+

03 March 2022

Source: vignettes/datasets.Rmd @@ -209,7 +209,7 @@ If you are reading this page from within R, please here.

+

It was last updated on 29 November 2021 11:38:23 UTC. Find more info about the structure of this data set here.

Direct download links:

  • Download as R file (1.3 MB)
    @@ -430,7 +430,7 @@ If you are reading this page from within R, please here.

    +

    It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set here.

    Direct download links:

    • Download as R file (0.2 MB)
      @@ -495,7 +495,7 @@ If you are reading this page from within R, please here.

      +

      It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set here.

      Direct download links:

      • Download as R file (33 kB)
        @@ -663,7 +663,7 @@ If you are reading this page from within R, please here.

        +

        It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set here.

        Direct download links:

        • Download as R file (5 kB)
          @@ -790,7 +790,7 @@ If you are reading this page from within R, please here.

          +

          It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set here.

          Direct download links:

          • Download as R file (78 kB)
            @@ -1057,7 +1057,7 @@ If you are reading this page from within R, please here.

            +

            It was last updated on 14 December 2021 21:59:33 UTC. Find more info about the structure of this data set here.

            Direct download links:

            • Download as R file (39 kB)
              @@ -1195,7 +1195,7 @@ If you are reading this page from within R, please here.

              +

              It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set here.

              Direct download links:

              • Download as R file (3 kB)
                diff --git a/docs/authors.html b/docs/authors.html index 2f372beae..61dddae52 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004
diff --git a/docs/index.html b/docs/index.html index 235810040..0383aef89 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004
diff --git a/docs/news/index.html b/docs/news/index.html index 7cc73e0ef..bc73adb46 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9002 + 1.8.0.9004
@@ -157,13 +157,13 @@
-

-AMR 1.8.0.9002

+

+AMR 1.8.0.9004

-

Last updated: 2 March 2022

+

Last updated: 3 March 2022

All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.

-

Changed

+

Changed

  • Support for antibiotic interpretations of the MIPS laboratory system: "U" for S (‘susceptible urine’), "D" for I (‘susceptible dose-dependent’)

  • Improved algorithm of as.mo(), especially for ignoring non-taxonomic text, such as:

    @@ -173,9 +173,11 @@ #> [1] "Staphylococcus aureus"

  • More informative warning messages

    • +

  • Added 192 as valid MIC

    • +

  • Updated MIC printing in tibbles

    • -

    Other

    +

    Other

    diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index 78933eab2..8b30fd9ed 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004
    diff --git a/docs/reference/WHOCC.html b/docs/reference/WHOCC.html index 6b749823f..a8777cd91 100644 --- a/docs/reference/WHOCC.html +++ b/docs/reference/WHOCC.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/ab_from_text.html b/docs/reference/ab_from_text.html index bb0ce37e2..45eebd4f8 100644 --- a/docs/reference/ab_from_text.html +++ b/docs/reference/ab_from_text.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/ab_property.html b/docs/reference/ab_property.html index ea4611cc6..8154f0f6e 100644 --- a/docs/reference/ab_property.html +++ b/docs/reference/ab_property.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/age.html b/docs/reference/age.html index 21f7400cd..0919d9491 100644 --- a/docs/reference/age.html +++ b/docs/reference/age.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html index d13568e85..d261d8df1 100644 --- a/docs/reference/age_groups.html +++ b/docs/reference/age_groups.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/antibiotic_class_selectors.html b/docs/reference/antibiotic_class_selectors.html index 6ec0aac78..4b1546852 100644 --- a/docs/reference/antibiotic_class_selectors.html +++ b/docs/reference/antibiotic_class_selectors.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index e84476d6f..132085292 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/as.ab.html b/docs/reference/as.ab.html index 5ccb64325..4e5153439 100644 --- a/docs/reference/as.ab.html +++ b/docs/reference/as.ab.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/as.disk.html b/docs/reference/as.disk.html index d303a6f9a..86ed111d9 100644 --- a/docs/reference/as.disk.html +++ b/docs/reference/as.disk.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/as.mic.html b/docs/reference/as.mic.html index e2ba15393..e181ea2a1 100644 --- a/docs/reference/as.mic.html +++ b/docs/reference/as.mic.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html index edaa414c3..7a226eb5e 100644 --- a/docs/reference/as.mo.html +++ b/docs/reference/as.mo.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 0fba532d1..b996975bb 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 @@ -264,7 +264,7 @@

    For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).

    -

    Thus, the guideline argument must be set to e.g., "EUCAST 2021" or "CLSI 2021". By simply using "EUCAST" (the default) or "CLSI" as input, the latest version of that guideline will automatically be selected. You can set your own data set using the reference_data argument. The guideline argument will then be ignored.

    +

    Thus, the guideline argument must be set to e.g., "EUCAST 2021" or "CLSI 2021". By simply using "EUCAST" (the default) or "CLSI" as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the reference_data argument. The guideline argument will then be ignored.

    diff --git a/docs/reference/atc_online.html b/docs/reference/atc_online.html index 7517a2d37..294df2e2f 100644 --- a/docs/reference/atc_online.html +++ b/docs/reference/atc_online.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004
    diff --git a/docs/reference/availability.html b/docs/reference/availability.html index dbe0e6637..87ab41f2f 100644 --- a/docs/reference/availability.html +++ b/docs/reference/availability.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/bug_drug_combinations.html b/docs/reference/bug_drug_combinations.html index f67f0fd6e..fc4f81dce 100644 --- a/docs/reference/bug_drug_combinations.html +++ b/docs/reference/bug_drug_combinations.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index 9b643fe42..b95a74249 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/catalogue_of_life_version.html b/docs/reference/catalogue_of_life_version.html index 7b30d7830..0adbedb76 100644 --- a/docs/reference/catalogue_of_life_version.html +++ b/docs/reference/catalogue_of_life_version.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/count.html b/docs/reference/count.html index de3564783..2e7935c71 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -18,7 +18,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible( AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/custom_eucast_rules.html b/docs/reference/custom_eucast_rules.html index aeb6399ac..8742d3b83 100644 --- a/docs/reference/custom_eucast_rules.html +++ b/docs/reference/custom_eucast_rules.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 86f9ad27a..b7b2aef0f 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -18,7 +18,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index b425f01d0..3ff142393 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -18,7 +18,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/g.test.html b/docs/reference/g.test.html index c58e29d62..829ec440e 100644 --- a/docs/reference/g.test.html +++ b/docs/reference/g.test.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/get_episode.html b/docs/reference/get_episode.html index 36ec98367..a2cbcd303 100644 --- a/docs/reference/get_episode.html +++ b/docs/reference/get_episode.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index c1453b667..6e56fe4c3 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html index 4e3f12462..d029323d9 100644 --- a/docs/reference/ggplot_rsi.html +++ b/docs/reference/ggplot_rsi.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/guess_ab_col.html b/docs/reference/guess_ab_col.html index 7a8fa3e91..db053ded4 100644 --- a/docs/reference/guess_ab_col.html +++ b/docs/reference/guess_ab_col.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/index.html b/docs/reference/index.html index 846ac6fba..1b4bab877 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/italicise_taxonomy.html b/docs/reference/italicise_taxonomy.html index 1ab453c63..563d1fc2e 100644 --- a/docs/reference/italicise_taxonomy.html +++ b/docs/reference/italicise_taxonomy.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/join.html b/docs/reference/join.html index dda9ddb1a..be01bef25 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/key_antimicrobials.html b/docs/reference/key_antimicrobials.html index 70a99226b..139c7aba4 100644 --- a/docs/reference/key_antimicrobials.html +++ b/docs/reference/key_antimicrobials.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/kurtosis.html b/docs/reference/kurtosis.html index d3e8a8dcc..eba28869b 100644 --- a/docs/reference/kurtosis.html +++ b/docs/reference/kurtosis.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/lifecycle.html b/docs/reference/lifecycle.html index bb3fe9782..7f49db42d 100644 --- a/docs/reference/lifecycle.html +++ b/docs/reference/lifecycle.html @@ -19,7 +19,7 @@ This page contains a section for every lifecycle (with text borrowed from the af AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/like.html b/docs/reference/like.html index 52d339177..54d6c6099 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index 006a53f26..25230bd23 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index f06589819..1bf7d57ce 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 1fa762aa4..205563339 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 66f85586f..12d26adb9 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/mo_matching_score.html b/docs/reference/mo_matching_score.html index f6dc27305..e8859d6bf 100644 --- a/docs/reference/mo_matching_score.html +++ b/docs/reference/mo_matching_score.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index c70cbf1ae..7651a5c4c 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/mo_source.html b/docs/reference/mo_source.html index 3b18c79ca..d2be9274c 100644 --- a/docs/reference/mo_source.html +++ b/docs/reference/mo_source.html @@ -18,7 +18,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/pca.html b/docs/reference/pca.html index 4893725c9..852c8c162 100644 --- a/docs/reference/pca.html +++ b/docs/reference/pca.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/plot.html b/docs/reference/plot.html index dbdf11f93..6927d23b1 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/proportion.html b/docs/reference/proportion.html index c37dad57a..2dfd113ea 100644 --- a/docs/reference/proportion.html +++ b/docs/reference/proportion.html @@ -18,7 +18,7 @@ resistance() should be used to calculate resistance, susceptibility() should be AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/random.html b/docs/reference/random.html index ef8be26a0..bfafecced 100644 --- a/docs/reference/random.html +++ b/docs/reference/random.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index dd4842572..d44740b9c 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/skewness.html b/docs/reference/skewness.html index 74902e5b7..cb12d060b 100644 --- a/docs/reference/skewness.html +++ b/docs/reference/skewness.html @@ -18,7 +18,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/reference/translate.html b/docs/reference/translate.html index 74be690a1..af9cd3d4f 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9001 + 1.8.0.9004 diff --git a/docs/survey.html b/docs/survey.html index 19418fea4..44606cd90 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -17,7 +17,7 @@ AMR (for R) - 1.8.0.9003 + 1.8.0.9004 diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index c240afd1d..8d55cec26 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -113,7 +113,7 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0 For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). -Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored. +Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored. } \subsection{After Interpretation}{