From c01dc8a5b721ab0575b788d0d36b19e18f10d193 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 23 Oct 2019 15:44:11 +0200 Subject: [PATCH] (v0.8.0.9003) printing fix for AB columns --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/guess_ab_col.R | 5 ++++- R/rsi.R | 7 +++---- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 8 ++++---- docs/reference/index.html | 2 +- 11 files changed, 19 insertions(+), 17 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 61c28a03..a51216b4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9002 +Version: 0.8.0.9003 Date: 2019-10-23 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 4a2e3d4a..3507d49a 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9002 +# AMR 0.8.0.9003 Last updated: 23-Oct-2019 ### Changes diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index 41a20189..971c707f 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -118,7 +118,7 @@ get_column_abx <- function(x, verbose = FALSE, ...) { - message(blue("NOTE: Auto-guessing columns suitable for analysis...")) + message(blue("NOTE: Auto-guessing columns suitable for analysis..."), appendLF = FALSE) x <- as.data.frame(x, stringsAsFactors = FALSE) x_bak <- x @@ -169,6 +169,9 @@ get_column_abx <- function(x, duplicates <- x[base::duplicated(x)] x <- x[!names(x) %in% names(duplicates)] + # succeeded with aut-guessing + message(blue("OK.")) + if (verbose == TRUE) { for (i in seq_len(length(x))) { message(blue(paste0("NOTE: Using column `", bold(x[i]), "` as input for `", names(x)[i], diff --git a/R/rsi.R b/R/rsi.R index b50bf01d..3748a3b6 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -504,14 +504,13 @@ type_sum.rsi <- function(x) { } #' @importFrom pillar pillar_shaft -#' @importFrom crayon bgGreen bgYellow bgRed black make_style +#' @importFrom crayon bgGreen bgYellow bgRed black white #' @export pillar_shaft.rsi <- function(x, ...) { out <- trimws(format(x)) out[is.na(x)] <- pillar::style_subtle(" NA") - real_white <- make_style(rgb(1, 1, 1)) - out[x == "S"] <- bgGreen(real_white(" S ")) + out[x == "S"] <- bgGreen(white(" S ")) out[x == "I"] <- bgYellow(black(" I ")) - out[x == "R"] <- bgRed(real_white(" R ")) + out[x == "R"] <- bgRed(white(" R ")) pillar::new_pillar_shaft_simple(out, align = "left", width = 3) } diff --git a/docs/404.html b/docs/404.html index 26c10b47..2dc63781 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 6b5043e5..eae10881 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 diff --git a/docs/articles/index.html b/docs/articles/index.html index fa130d77..ed6229f1 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 diff --git a/docs/authors.html b/docs/authors.html index aa0dee2c..0dd667f8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 diff --git a/docs/index.html b/docs/index.html index 6fa4c622..044705a3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 diff --git a/docs/news/index.html b/docs/news/index.html index 9232416b..0916eaff 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003 @@ -231,9 +231,9 @@ -
+

-AMR 0.8.0.9002 Unreleased +AMR 0.8.0.9003 Unreleased

Last updated: 23-Oct-2019

@@ -1309,7 +1309,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.8.0.9002
    • +
  • 0.8.0.9003
  • 0.8.0
  • 0.7.1
  • 0.7.0
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ae348ec..9aed8bd1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9002 + 0.8.0.9003