From 4f94e1312f11328e8b62238d2c4371be78255f14 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Thu, 11 Jun 2020 20:03:13 +0200 Subject: [PATCH] (v1.2.0.9006) improve auto col-determination --- DESCRIPTION | 4 ++-- NEWS.md | 5 +++-- R/aa_helper_functions.R | 39 ++++++++++++++------------------- 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 | 14 +++++++----- docs/pkgdown.yml | 2 +- docs/reference/antibiotics.html | 2 +- docs/reference/index.html | 2 +- 12 files changed, 38 insertions(+), 40 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f51edcf7..2f8fe91d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.2.0.9005 -Date: 2020-06-09 +Version: 1.2.0.9006 +Date: 2020-06-11 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index f0eb7c52..dd1ee8a2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.2.0.9005 -## Last updated: 09-Jun-2020 +# AMR 1.2.0.9006 +## Last updated: 11-Jun-2020 ### Changed * Fixed a bug where `eucast_rules()` would not work on a tibble when the `tibble` or `dplyr` package was loaded @@ -9,6 +9,7 @@ * Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*) * Added official antimicrobial names to all `filter_ab_class()` functions, such as `filter_aminoglycosides()` * Added antibiotics code "FOX1" for cefoxitin screening (abbreviation "cfsc") to the `antibiotics` data set +* Improved auto-determination for columns of types and # AMR 1.2.0 diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index 8c926c2f..b947fd77 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -103,60 +103,55 @@ search_type_in_df <- function(x, type) { # -- mo if (type == "mo") { - if ("mo" %in% lapply(x, class)) { - found <- colnames(x)[lapply(x, class) == "mo"][1] + if (any(sapply(x, is.mo))) { + found <- sort(colnames(x)[sapply(x, is.mo)])[1] } else if ("mo" %in% colnames(x) & suppressWarnings( all(x$mo %in% c(NA, microorganisms$mo, microorganisms.translation$mo_old)))) { found <- "mo" - } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) { - found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1] - } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) { - found <- colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)"][1] + } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) { + found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1] + } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) { + found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1] } else if (any(colnames(x) %like% "species")) { - found <- colnames(x)[colnames(x) %like% "species"][1] + found <- sort(colnames(x)[colnames(x) %like% "species"])[1] } } # -- key antibiotics if (type == "keyantibiotics") { if (any(colnames(x) %like% "^key.*(ab|antibiotics)")) { - found <- colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"][1] + found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"])[1] } } # -- date if (type == "date") { if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) { # WHONET support - found <- colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"][1] + found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1] if (!any(class(pull(x, found)) %in% c("Date", "POSIXct"))) { stop(font_red(paste0("ERROR: Found column `", font_bold(found), "` to be used as input for `col_", type, - "`, but this column contains no valid dates. Transform its values to valid dates first.")), + "`, but this column contains no valid dates. Transform its values to valid dates first.")), call. = FALSE) } - } else { - for (i in seq_len(ncol(x))) { - if (any(class(pull(x, i)) %in% c("Date", "POSIXct"))) { - found <- colnames(x)[i] - break - } - } + } else if (any(sapply(x, function(x) inherits(x, c("Date", "POSIXct"))))) { + found <- sort(colnames(x)[sapply(x, function(x) inherits(x, c("Date", "POSIXct")))])[1] } } # -- patient id if (type == "patient_id") { if (any(colnames(x) %like% "^(identification |patient|patid)")) { - found <- colnames(x)[colnames(x) %like% "^(identification |patient|patid)"][1] + found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1] } } # -- specimen if (type == "specimen") { if (any(colnames(x) %like% "(specimen type|spec_type)")) { - found <- colnames(x)[colnames(x) %like% "(specimen type|spec_type)"][1] + found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1] } else if (any(colnames(x) %like% "^(specimen)")) { - found <- colnames(x)[colnames(x) %like% "^(specimen)"][1] + found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1] } } # -- UTI (urinary tract infection) @@ -164,13 +159,13 @@ search_type_in_df <- function(x, type) { if (any(colnames(x) == "uti")) { found <- colnames(x)[colnames(x) == "uti"][1] } else if (any(colnames(x) %like% "(urine|urinary)")) { - found <- colnames(x)[colnames(x) %like% "(urine|urinary)"][1] + found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1] } if (!is.null(found)) { # this column should contain logicals if (!is.logical(x[, found, drop = TRUE])) { message(font_red(paste0("NOTE: Column `", font_bold(found), "` found as input for `col_", type, - "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored."))) + "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored."))) found <- NULL } } diff --git a/docs/404.html b/docs/404.html index ab132b94..a674a1f9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e281e91f..b08bef1a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9a1e44dc..cbd03f55 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 diff --git a/docs/authors.html b/docs/authors.html index bffcaf94..ed6ba49f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 diff --git a/docs/index.html b/docs/index.html index dabe1a1a..a4c8bb6f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 diff --git a/docs/news/index.html b/docs/news/index.html index 2e8a2ebb..e7000407 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006 @@ -229,13 +229,13 @@ Source: NEWS.md -
-

-AMR 1.2.0.9005 Unreleased +
+

+AMR 1.2.0.9006 Unreleased

-
+

-Last updated: 09-Jun-2020 +Last updated: 11-Jun-2020

@@ -250,6 +250,8 @@
  • Added official antimicrobial names to all filter_ab_class() functions, such as filter_aminoglycosides()
  • Added antibiotics code “FOX1” for cefoxitin screening (abbreviation “cfsc”) to the antibiotics data set
    • +
  • Improved auto-determination for columns of types and +

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e9cacef0..373d9ea5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-06-09T14:30Z +last_built: 2020-06-11T17:56Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 302b0b4f..d6f585e9 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0.9004 + 1.2.0.9006
    diff --git a/docs/reference/index.html b/docs/reference/index.html index 08eaa068..274ff04c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9005 + 1.2.0.9006