diff --git a/DESCRIPTION b/DESCRIPTION index ef94af94..35856262 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9013 +Version: 0.8.0.9014 Date: 2019-11-05 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 28a8d58c..c05aec11 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9013 +# AMR 0.8.0.9014 Last updated: 05-Nov-2019 ### New diff --git a/R/mdro.R b/R/mdro.R index 8895f090..3ae7752d 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -298,8 +298,7 @@ mdro <- function(x, "PLB", "TCY", "DOX", - "MNO" - ), + "MNO"), verbose = verbose, ...) } else if (guideline$code == "tb") { cols_ab <- get_column_abx(x = x, @@ -442,7 +441,6 @@ mdro <- function(x, cols <- cols[!ab_missing(cols)] cols <- cols[!is.na(cols)] if (length(rows) > 0 & length(cols) > 0) { - #print(cols) x <<- x %>% mutate_at(vars(cols), as.rsi) x[rows, "columns_nonsusceptible"] <<- sapply(rows, function(row, group_vct = cols) { @@ -905,8 +903,7 @@ mdro <- function(x, } x[which( x$fullname %like% "Pseudomonas aeruginosa" - & x$psae >= 3 - ), "MDRO"] <- 3 + & x$psae >= 3), "MDRO"] <- 3 # Table 3 trans_tbl(3, @@ -990,7 +987,7 @@ mdro <- function(x, } # some more info on negative results - if (verbose == TRUE ) { + if (verbose == TRUE) { if (guideline$code == "cmi2012") { x[which(x$MDRO == 1 & !is.na(x$classes_affected)), "reason"] <- paste0(x$classes_affected[which(x$MDRO == 1 & !is.na(x$classes_affected))], " of ", x$classes_available[which(x$MDRO == 1 & !is.na(x$classes_affected))], " available classes contain R or I (3 required for MDR)") } else { diff --git a/appveyor.yml b/appveyor.yml index f82022c8..920694a4 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -39,7 +39,7 @@ environment: GCC_PATH: mingw_64 WARNINGS_ARE_ERRORS: 1 PKGTYPE: win.binary - # USE_RTOOLS: true + USE_RTOOLS: true matrix: - R_VERSION: release diff --git a/docs/404.html b/docs/404.html index c9bfadea..663e0fe2 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5614b6d1..e772925c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 diff --git a/docs/articles/index.html b/docs/articles/index.html index 768e0550..61f957ce 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 diff --git a/docs/authors.html b/docs/authors.html index 1f865cdc..0fd448c1 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 diff --git a/docs/index.html b/docs/index.html index 27f40724..b0439b58 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 diff --git a/docs/news/index.html b/docs/news/index.html index 569182dd..12f6c888 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014 @@ -231,9 +231,9 @@ -
+

-AMR 0.8.0.9013 Unreleased +AMR 0.8.0.9014 Unreleased

Last updated: 05-Nov-2019

@@ -1333,7 +1333,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.8.0.9013
    • +
  • 0.8.0.9014
  • 0.8.0
  • 0.7.1
  • 0.7.0
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 30348d0c..9b761b3f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9013 + 0.8.0.9014