diff --git a/DESCRIPTION b/DESCRIPTION index 8a3d1b00..bf019825 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.3.0.9019 +Version: 1.3.0.9020 Date: 2020-09-14 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 072b9d3d..75dd9af2 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.3.0.9019 +# AMR 1.3.0.9020 ## Last updated: 14 September 2020 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly! diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 5f266850..cf1db637 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -221,6 +221,7 @@ eucast_rules <- function(x, col_mo <- search_type_in_df(x = x, type = "mo") } stop_if(is.null(col_mo), "`col_mo` must be set") + stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found") stop_ifnot(all(rules %in% c("breakpoints", "expert", "other", "all")), '`rules` must be one or more of: "breakpoints", "expert", "other", "all".') diff --git a/R/first_isolate.R b/R/first_isolate.R index c616ad21..4403ee20 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -167,6 +167,7 @@ first_isolate <- function(x, if (is.null(col_mo)) { col_mo <- search_type_in_df(x = x, type = "mo") stop_if(is.null(col_mo), "`col_mo` must be set") + stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found") } # -- date diff --git a/R/mdro.R b/R/mdro.R index ffdb0185..ded70344 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -150,6 +150,7 @@ mdro <- function(x, col_mo <- "mo" } stop_if(is.null(col_mo), "`col_mo` must be set") + stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found") if (guideline$code == "cmi2012") { guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." diff --git a/R/mo.R b/R/mo.R index 085c4abd..6f2e0063 100755 --- a/R/mo.R +++ b/R/mo.R @@ -288,6 +288,7 @@ exec_as.mo <- function(x, actual_uncertainty = 1, actual_input = NULL, language = get_locale()) { + check_dataset_integrity() lookup <- function(needle, @@ -298,7 +299,7 @@ exec_as.mo <- function(x, initial = initial_search, uncertainty = actual_uncertainty, input_actual = actual_input) { - + if (!is.null(input_actual)) { input <- input_actual } else { @@ -312,7 +313,7 @@ exec_as.mo <- function(x, } if (length(column) == 1) { res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE] - if (NROW(res_df) > 1) { + if (NROW(res_df) > 1 & uncertainty != -1) { # sort the findings on matching score res_df <- res_df[order(mo_matching_score(input, res_df[, "fullname", drop = TRUE]), decreasing = TRUE), , drop = FALSE] } @@ -326,8 +327,8 @@ exec_as.mo <- function(x, if (isTRUE(debug_mode)) { cat(font_green(paste0(" **MATCH** (", NROW(res_df), " results)\n"))) } - if (length(res) > n | uncertainty > 1) { - # save the other possible results as well + if ((length(res) > n | uncertainty > 1) & uncertainty != -1) { + # save the other possible results as well, but not for forced certain results (then uncertainty == -1) uncertainties <<- rbind(uncertainties, format_uncertainty_as_df(uncertainty_level = uncertainty, input = input, @@ -437,7 +438,7 @@ exec_as.mo <- function(x, # we need special treatment for very prevalent full names, they are likely! # e.g. as.mo("Staphylococcus aureus") x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE] - + } else if (all(x %in% reference_data_to_use$fullname)) { # we need special treatment for very prevalent full names, they are likely! # e.g. as.mo("Staphylococcus aureus") @@ -702,18 +703,18 @@ exec_as.mo <- function(x, # translate known trivial abbreviations to genus + species ---- if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA") | x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") { - x[i] <- lookup(fullname == "Staphylococcus aureus") + x[i] <- lookup(fullname == "Staphylococcus aureus", uncertainty = -1) next } if (toupper(x_backup_without_spp[i]) %in% c("MRSE", "MSSE") | x_backup_without_spp[i] %like_case% " (mrse|msse) ") { - x[i] <- lookup(fullname == "Staphylococcus epidermidis") + x[i] <- lookup(fullname == "Staphylococcus epidermidis", uncertainty = -1) next } if (toupper(x_backup_without_spp[i]) == "VRE" | x_backup_without_spp[i] %like_case% " vre " | x_backup_without_spp[i] %like_case% "(enterococci|enterokok|enterococo)[a-z]*?$") { - x[i] <- lookup(genus == "Enterococcus") + x[i] <- lookup(genus == "Enterococcus", uncertainty = -1) next } # support for: @@ -731,50 +732,50 @@ exec_as.mo <- function(x, if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC") # also support O-antigens of E. coli: O26, O103, O104, O111, O121, O145, O157 | x_backup_without_spp[i] %like_case% "o?(26|103|104|111|121|145|157)") { - x[i] <- lookup(fullname == "Escherichia coli") + x[i] <- lookup(fullname == "Escherichia coli", uncertainty = -1) next } if (toupper(x_backup_without_spp[i]) == "MRPA" | x_backup_without_spp[i] %like_case% " mrpa ") { # multi resistant P. aeruginosa - x[i] <- lookup(fullname == "Pseudomonas aeruginosa") + x[i] <- lookup(fullname == "Pseudomonas aeruginosa", uncertainty = -1) next } if (toupper(x_backup_without_spp[i]) == "CRSM") { # co-trim resistant S. maltophilia - x[i] <- lookup(fullname == "Stenotrophomonas maltophilia") + x[i] <- lookup(fullname == "Stenotrophomonas maltophilia", uncertainty = -1) next } if (toupper(x_backup_without_spp[i]) %in% c("PISP", "PRSP", "VISP", "VRSP") | x_backup_without_spp[i] %like_case% " (pisp|prsp|visp|vrsp) ") { # peni I, peni R, vanco I, vanco R: S. pneumoniae - x[i] <- lookup(fullname == "Streptococcus pneumoniae") + x[i] <- lookup(fullname == "Streptococcus pneumoniae", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "^g[abcdfghk]s$") { # Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB) x[i] <- lookup(mo == toupper(gsub("g([abcdfghk])s", "B_STRPT_GRP\\1", - x_backup_without_spp[i]))) + x_backup_without_spp[i])), uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "(streptococ|streptokok).* [abcdfghk]$") { # Streptococci in different languages, like "estreptococos grupo B" x[i] <- lookup(mo == toupper(gsub(".*(streptococ|streptokok|estreptococ).* ([abcdfghk])$", "B_STRPT_GRP\\2", - x_backup_without_spp[i]))) + x_backup_without_spp[i])), uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "group [abcdfghk] (streptococ|streptokok|estreptococ)") { # Streptococci in different languages, like "Group A Streptococci" x[i] <- lookup(mo == toupper(gsub(".*group ([abcdfghk]) (streptococ|streptokok|estreptococ).*", "B_STRPT_GRP\\1", - x_backup_without_spp[i]))) + x_backup_without_spp[i])), uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "haemoly.*strept") { # Haemolytic streptococci in different languages - x[i] <- lookup(mo == "B_STRPT_HAEM") + x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1) next } # CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ---- @@ -782,14 +783,14 @@ exec_as.mo <- function(x, | x_trimmed[i] %like_case% "[ck]oagulas[ea] negatie?[vf]" | x_backup_without_spp[i] %like_case% "[ck]o?ns[^a-z]?$") { # coerce S. coagulase negative - x[i] <- lookup(mo == "B_STPHY_CONS") + x[i] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "[ck]oagulas[ea] positie?[vf]" | x_trimmed[i] %like_case% "[ck]oagulas[ea] positie?[vf]" | x_backup_without_spp[i] %like_case% "[ck]o?ps[^a-z]?$") { # coerce S. coagulase positive - x[i] <- lookup(mo == "B_STPHY_COPS") + x[i] <- lookup(mo == "B_STPHY_COPS", uncertainty = -1) next } # streptococcal groups: milleri and viridans @@ -797,50 +798,50 @@ exec_as.mo <- function(x, | x_backup_without_spp[i] %like_case% "strepto.* mil+er+i" | x_backup_without_spp[i] %like_case% "mgs[^a-z]?$") { # Milleri Group Streptococcus (MGS) - x[i] <- lookup(mo == "B_STRPT_MILL") + x[i] <- lookup(mo == "B_STRPT_MILL", uncertainty = -1) next } if (x_trimmed[i] %like_case% "strepto.* viridans" | x_backup_without_spp[i] %like_case% "strepto.* viridans" | x_backup_without_spp[i] %like_case% "vgs[^a-z]?$") { # Viridans Group Streptococcus (VGS) - x[i] <- lookup(mo == "B_STRPT_VIRI") + x[i] <- lookup(mo == "B_STRPT_VIRI", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "gram[ -]?neg.*" | x_backup_without_spp[i] %like_case% "negatie?[vf]" | x_trimmed[i] %like_case% "gram[ -]?neg.*") { # coerce Gram negatives - x[i] <- lookup(mo == "B_GRAMN") + x[i] <- lookup(mo == "B_GRAMN", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "gram[ -]?pos.*" | x_backup_without_spp[i] %like_case% "positie?[vf]" | x_trimmed[i] %like_case% "gram[ -]?pos.*") { # coerce Gram positives - x[i] <- lookup(mo == "B_GRAMP") + x[i] <- lookup(mo == "B_GRAMP", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "mycoba[ck]teri.[nm]?$") { # coerce mycobacteria in multiple languages - x[i] <- lookup(genus == "Mycobacterium") + x[i] <- lookup(genus == "Mycobacterium", uncertainty = -1) next } if (x_backup_without_spp[i] %like_case% "salmonella [a-z]+ ?.*") { if (x_backup_without_spp[i] %like_case% "salmonella group") { # Salmonella Group A to Z, just return S. species for now - x[i] <- lookup(genus == "Salmonella") + x[i] <- lookup(genus == "Salmonella", uncertainty = -1) next } else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) & !x_backup[i] %like% "t[iy](ph|f)[iy]") { # Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica # except for S. typhi, S. paratyphi, S. typhimurium - x[i] <- lookup(fullname == "Salmonella enterica") + x[i] <- lookup(fullname == "Salmonella enterica", uncertainty = -1) uncertainties <- rbind(uncertainties, format_uncertainty_as_df(uncertainty_level = 1, input = x_backup[i], - result_mo = lookup(fullname == "Salmonella enterica", "mo"))) + result_mo = lookup(fullname == "Salmonella enterica", "mo", uncertainty = -1))) next } } @@ -848,17 +849,17 @@ exec_as.mo <- function(x, # trivial names known to the field: if ("meningococcus" %like_case% x_trimmed[i]) { # coerce Neisseria meningitidis - x[i] <- lookup(fullname == "Neisseria meningitidis") + x[i] <- lookup(fullname == "Neisseria meningitidis", uncertainty = -1) next } if ("gonococcus" %like_case% x_trimmed[i]) { # coerce Neisseria gonorrhoeae - x[i] <- lookup(fullname == "Neisseria gonorrhoeae") + x[i] <- lookup(fullname == "Neisseria gonorrhoeae", uncertainty = -1) next } if ("pneumococcus" %like_case% x_trimmed[i]) { # coerce Streptococcus penumoniae - x[i] <- lookup(fullname == "Streptococcus pneumoniae") + x[i] <- lookup(fullname == "Streptococcus pneumoniae", uncertainty = -1) next } # } @@ -1246,13 +1247,11 @@ exec_as.mo <- function(x, } if (!empty_result(found)) { found_result <- found - found <- lookup(mo == found) # uncertainty level 2 only if searched part contains a space (otherwise it will be found with lvl 3) if (x_strip_collapsed %like_case% " ") { uncertainties <<- rbind(uncertainties, - format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level, - input = a.x_backup, - result_mo = found_result)) + attr(found, which = "uncertainties", exact = TRUE)) + found <- lookup(mo == found) return(found) } } @@ -1283,11 +1282,9 @@ exec_as.mo <- function(x, } if (!empty_result(found)) { found_result <- found - found <- lookup(mo == found) uncertainties <<- rbind(uncertainties, - format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level, - input = a.x_backup, - result_mo = found_result)) + attr(found, which = "uncertainties", exact = TRUE)) + found <- lookup(mo == found) return(found) } } @@ -1311,11 +1308,9 @@ exec_as.mo <- function(x, } if (!empty_result(found)) { found_result <- found - found <- lookup(mo == found) uncertainties <<- rbind(uncertainties, - format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level, - input = a.x_backup, - result_mo = found_result)) + attr(found, which = "uncertainties", exact = TRUE)) + found <- lookup(mo == found) return(found) } } @@ -1332,9 +1327,8 @@ exec_as.mo <- function(x, if (!is.na(found) & nchar(g.x_backup_without_spp) >= 6) { found_result <- lookup(mo == found) uncertainties <<- rbind(uncertainties, - format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level, - input = a.x_backup, - result_mo = found_result)) + attr(found, which = "uncertainties", exact = TRUE)) + found <- lookup(mo == found) return(found) } } @@ -1388,7 +1382,7 @@ exec_as.mo <- function(x, # no results found: make them UNKNOWN ---- - x[i] <- lookup(mo == "UNKNOWN") + x[i] <- lookup(mo == "UNKNOWN", uncertainty = -1) if (initial_search == TRUE) { failures <- c(failures, x_backup[i]) } @@ -1478,33 +1472,33 @@ exec_as.mo <- function(x, immediate. = TRUE) } - x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS") - x[x %in% CoPS] <- lookup(mo == "B_STPHY_COPS") + x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1) + x[x %in% CoPS] <- lookup(mo == "B_STPHY_COPS", uncertainty = -1) if (Becker == "all") { - x[x %in% lookup(fullname %like_case% "^Staphylococcus aureus", n = Inf)] <- lookup(mo == "B_STPHY_COPS") + x[x %in% lookup(fullname %like_case% "^Staphylococcus aureus", n = Inf)] <- lookup(mo == "B_STPHY_COPS", uncertainty = -1) } } # Lancefield ---- if (Lancefield == TRUE | Lancefield == "all") { # group A - S. pyogenes - x[x %in% lookup(genus == "Streptococcus" & species == "pyogenes", n = Inf)] <- lookup(fullname == "Streptococcus group A") + x[x %in% lookup(genus == "Streptococcus" & species == "pyogenes", n = Inf)] <- lookup(fullname == "Streptococcus group A", uncertainty = -1) # group B - S. agalactiae - x[x %in% lookup(genus == "Streptococcus" & species == "agalactiae", n = Inf)] <- lookup(fullname == "Streptococcus group B") + x[x %in% lookup(genus == "Streptococcus" & species == "agalactiae", n = Inf)] <- lookup(fullname == "Streptococcus group B", uncertainty = -1) # group C x[x %in% lookup(genus == "Streptococcus" & species %in% c("equisimilis", "equi", "zooepidemicus", "dysgalactiae"), - n = Inf)] <- lookup(fullname == "Streptococcus group C") + n = Inf)] <- lookup(fullname == "Streptococcus group C", uncertainty = -1) if (Lancefield == "all") { # all Enterococci - x[x %in% lookup(genus == "Enterococcus", n = Inf)] <- lookup(fullname == "Streptococcus group D") + x[x %in% lookup(genus == "Enterococcus", n = Inf)] <- lookup(fullname == "Streptococcus group D", uncertainty = -1) } # group F - S. anginosus - x[x %in% lookup(genus == "Streptococcus" & species == "anginosus", n = Inf)] <- lookup(fullname == "Streptococcus group F") + x[x %in% lookup(genus == "Streptococcus" & species == "anginosus", n = Inf)] <- lookup(fullname == "Streptococcus group F", uncertainty = -1) # group H - S. sanguinis - x[x %in% lookup(genus == "Streptococcus" & species == "sanguinis", n = Inf)] <- lookup(fullname == "Streptococcus group H") + x[x %in% lookup(genus == "Streptococcus" & species == "sanguinis", n = Inf)] <- lookup(fullname == "Streptococcus group H", uncertainty = -1) # group K - S. salivarius - x[x %in% lookup(genus == "Streptococcus" & species == "salivarius", n = Inf)] <- lookup(fullname == "Streptococcus group K") + x[x %in% lookup(genus == "Streptococcus" & species == "salivarius", n = Inf)] <- lookup(fullname == "Streptococcus group K", uncertainty = -1) } # Wrap up ---------------------------------------------------------------- @@ -1533,10 +1527,20 @@ exec_as.mo <- function(x, print(mo_renamed()) } - if (NROW(uncertainties) > 0 & initial_search == FALSE) { + if (initial_search == FALSE) { + # we got here from uncertain_fn(). + if (NROW(uncertainties) == 0) { + # the stripped/transformed version of x_backup is apparently a full hit, like with: as.mo("Escherichia (hello there) coli") + uncertainties <- rbind(uncertainties, + format_uncertainty_as_df(uncertainty_level = actual_uncertainty, + input = actual_input, + result_mo = x, + candidates = "")) + } # this will save the uncertain items as attribute, so they can be bound to `uncertainties` in the uncertain_fn() function x <- structure(x, uncertainties = uncertainties) } + if (old_mo_warning == TRUE & property != "mo") { warning("The input contained old microorganism IDs from previous versions of this package.\nPlease use `as.mo()` on these old IDs to transform them to the new format.\nSUPPORT FOR THIS WILL BE DROPPED IN A FUTURE VERSION.", call. = FALSE) @@ -1748,7 +1752,8 @@ print.mo_uncertainties <- function(x, ...) { if (NROW(x) == 0) { return(NULL) } - cat(font_blue("Scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name.\n")) + cat(font_blue(strwrap(c("Scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. Furthermore, an indication is given about the likelihood of the match - the more transformations are needed for coercion, the more unlikely the result.")), collapse = "\n")) + cat("\n") msg <- "" for (i in seq_len(nrow(x))) { @@ -1763,17 +1768,25 @@ print.mo_uncertainties <- function(x, ...) { candidates <- paste(candidates, collapse = ", ") # align with input after arrow candidates <- paste0("\n", strrep(" ", nchar(x[i, ]$input) + 6), - "Other", ifelse(n_candidates == 25, " (max 25)", ""), ": ", candidates) + "Less likely", ifelse(n_candidates == 25, " (max 25)", ""), ": ", candidates) } else { candidates <- "" } + if (x[i, ]$uncertainty == 1) { + uncertainty_interpretation <- font_green("* VERY LIKELY *") + } else if (x[i, ]$uncertainty == 1) { + uncertainty_interpretation <- font_orange("* LIKELY *") + } else { + uncertainty_interpretation <- font_red("* UNLIKELY *") + } msg <- paste(msg, paste0('"', x[i, ]$input, '" -> ', paste0(font_bold(font_italic(x[i, ]$fullname)), ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""), " (", x[i, ]$mo, ", score: ", trimws(percentage(mo_matching_score(x[i, ]$input, x[i, ]$fullname) * (1 / x[i, ]$uncertainty), digits = 1)), - ")"), + ") "), + uncertainty_interpretation, candidates), sep = "\n") } @@ -1877,7 +1890,7 @@ mo_matching_score <- function(input, fullname) { dist <- (nchar(fullname) - 0.5 * levenshtein) / nchar(fullname) index_in_MO_lookup <- tryCatch((nrow(MO_lookup) - match(fullname, MO_lookup$fullname)) / nrow(MO_lookup), error = function(e) rep(1, length(fullname))) - dist * index_in_MO_lookup + (0.25 * dist) + (0.75 * index_in_MO_lookup) } trimws2 <- function(x) { diff --git a/R/translate.R b/R/translate.R index 40956ddd..9d3c9d5d 100755 --- a/R/translate.R +++ b/R/translate.R @@ -30,7 +30,7 @@ #' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations). #' #' ## Changing the default language -#' The system language will be used at default (as returned by [Sys.getenv("LANG")] or, if `LANG` is not set, [Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order: +#' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order: #' #' 1. Setting the R option `AMR_locale`, e.g. by running `options(AMR_locale = "de")` #' 2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory diff --git a/docs/404.html b/docs/404.html index 391dc047..72cfdcfc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f2039627..edcf50c7 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 diff --git a/docs/articles/index.html b/docs/articles/index.html index 806c3561..2496970e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 diff --git a/docs/authors.html b/docs/authors.html index 473eb5d0..74706310 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 diff --git a/docs/index.html b/docs/index.html index 55ffccdf..0ffe2459 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 diff --git a/docs/news/index.html b/docs/news/index.html index b8f7e743..4cc3d73a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.3.0.9019 Unreleased +
+

+AMR 1.3.0.9020 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 08d97a9d..8bb0600d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.7.3 pkgdown: 1.5.1.9000 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f articles: [] -last_built: 2020-09-14T11:57Z +last_built: 2020-09-14T17:41Z 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 39d6ba49..cd7bf27b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020

diff --git a/docs/reference/translate.html b/docs/reference/translate.html index eccec3d2..8c9167e7 100644 --- a/docs/reference/translate.html +++ b/docs/reference/translate.html @@ -50,7 +50,7 @@ - + @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9018 + 1.3.0.9020
@@ -252,7 +252,7 @@

Please suggest your own translations by creating a new issue on our repository.

Changing the default language

-

The system language will be used at default (as returned by Sys.getenv("LANG") or, if LANG is not set, Sys.getlocale()), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:

    +

    The system language will be used at default (as returned by Sys.getenv("LANG") or, if LANG is not set, Sys.getlocale()), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:

    1. Setting the R option AMR_locale, e.g. by running options(AMR_locale = "de")

    2. Setting the system variable LANGUAGE or LANG, e.g. by adding LANGUAGE="de_DE.utf8" to your .Renviron file in your home directory

    diff --git a/docs/survey.html b/docs/survey.html index eafb345c..6cd06444 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9019 + 1.3.0.9020
diff --git a/man/translate.Rd b/man/translate.Rd index ec0c5547..a817c9b2 100644 --- a/man/translate.Rd +++ b/man/translate.Rd @@ -18,7 +18,7 @@ Currently supported languages are: Dutch, English, French, German, Italian, Port Please suggest your own translations \href{https://github.com/msberends/AMR/issues/new?title=Translations}{by creating a new issue on our repository}. \subsection{Changing the default language}{ -The system language will be used at default (as returned by \link{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale()}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order: +The system language will be used at default (as returned by \code{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale()}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order: \enumerate{ \item Setting the R option \code{AMR_locale}, e.g. by running \code{options(AMR_locale = "de")} \item Setting the system variable \code{LANGUAGE} or \code{LANG}, e.g. by adding \code{LANGUAGE="de_DE.utf8"} to your \code{.Renviron} file in your home directory diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index f5542a5b..cf652da2 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -205,8 +205,8 @@ test_that("as.mo works", { expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN") expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE)) expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS") - expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY") - expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS") + expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS") + expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS_ANRB") # predefined reference_df expect_equal(as.character(as.mo("TestingOwnID", @@ -228,15 +228,15 @@ test_that("as.mo works", { c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")) # hard to find - expect_equal(as.character(suppressWarnings(as.mo( + expect_equal(as.character(suppressMessages(as.mo( c("Microbacterium paraoxidans", "Streptococcus suis (bovis gr)", "Raoultella (here some text) terrigena")))), c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")) expect_output(print(mo_uncertainties())) - + # Salmonella (City) are all actually Salmonella enterica spp (City) - expect_equal(suppressWarnings(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))), + expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))), c("Salmonella enterica", "Salmonella enterica", "Salmonella")) # no virusses