diff --git a/DESCRIPTION b/DESCRIPTION index bce7122e..6dd34bb6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9031 +Version: 0.8.0.9032 Date: 2019-11-15 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index a8d7cf91..7a5ce649 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9031 +# AMR 0.8.0.9032 Last updated: 15-Nov-2019 ### Breaking @@ -35,7 +35,7 @@ as.mo(c("Stafylococcus aureus", "staphylokok aureuz")) #> Warning: - #> Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them. + #> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them. #> Class 'mo' #> [1] B_STPHY_AURS B_STPHY_AURS diff --git a/R/mo.R b/R/mo.R index bad263d4..3f44bd27 100755 --- a/R/mo.R +++ b/R/mo.R @@ -545,7 +545,7 @@ exec_as.mo <- function(x, x <- gsub("o+", "o+", x) x <- gsub("(.)\\1+", "\\1+", x) # allow multiplication of all other consonants - x <- gsub("([bdghjlnrw]+)", "\\1+", x) + x <- gsub("([bdgjlnrw]+)", "\\1+", x) # allow ending in -en or -us x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, perl = TRUE) # if the input is longer than 10 characters, allow any forgotten consonant between all characters, as some might just have forgotten one... @@ -555,10 +555,11 @@ exec_as.mo <- function(x, # allow au and ou after all these regex implementations x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE) x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE) - # make sure to remove regex overkill (will lead to errors) - x <- gsub("++", "+", x, fixed = TRUE) } x <- strip_whitespace(x, dyslexia_mode) + # make sure to remove regex overkill (will lead to errors) + x <- gsub("++", "+", x, fixed = TRUE) + x <- gsub("?+", "?", x, fixed = TRUE) x_trimmed <- x x_trimmed_species <- paste(x_trimmed, "species") @@ -571,21 +572,22 @@ exec_as.mo <- function(x, # add start en stop regex x <- paste0("^", x, "$") + x_withspaces_start_only <- paste0("^", x_withspaces) x_withspaces_end_only <- paste0(x_withspaces, "$") x_withspaces_start_end <- paste0("^", x_withspaces, "$") if (isTRUE(debug)) { - cat(paste0('x "', x, '"\n')) - cat(paste0('x_species "', x_species, '"\n')) - cat(paste0('x_withspaces_start_only "', x_withspaces_start_only, '"\n')) - cat(paste0('x_withspaces_end_only "', x_withspaces_end_only, '"\n')) - cat(paste0('x_withspaces_start_end "', x_withspaces_start_end, '"\n')) - cat(paste0('x_backup "', x_backup, '"\n')) - cat(paste0('x_backup_without_spp "', x_backup_without_spp, '"\n')) - cat(paste0('x_trimmed "', x_trimmed, '"\n')) - cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n')) - cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n')) + cat(paste0(blue('x'), ' "', x, '"\n')) + cat(paste0(blue('x_species'), ' "', x_species, '"\n')) + cat(paste0(blue('x_withspaces_start_only'), ' "', x_withspaces_start_only, '"\n')) + cat(paste0(blue('x_withspaces_end_only'), ' "', x_withspaces_end_only, '"\n')) + cat(paste0(blue('x_withspaces_start_end'), ' "', x_withspaces_start_end, '"\n')) + cat(paste0(blue('x_backup'), ' "', x_backup, '"\n')) + cat(paste0(blue('x_backup_without_spp'), ' "', x_backup_without_spp, '"\n')) + cat(paste0(blue('x_trimmed'), ' "', x_trimmed, '"\n')) + cat(paste0(blue('x_trimmed_species'), ' "', x_trimmed_species, '"\n')) + cat(paste0(blue('x_trimmed_without_group'), ' "', x_trimmed_without_group, '"\n')) } progress <- progress_estimated(n = length(x), min_time = 3) @@ -1590,12 +1592,12 @@ exec_as.mo <- function(x, if (NROW(uncertainties) > 0 & initial_search == TRUE) { options(mo_uncertainties = as.list(distinct(uncertainties, input, .keep_all = TRUE))) - plural <- c("", "it") + plural <- c("", "it", "was") if (NROW(uncertainties) > 1) { - plural <- c("s", "them") + plural <- c("s", "them", "were") } msg <- paste0("\nResult", plural[1], " of ", nr2char(NROW(uncertainties)), " value", plural[1], - " was guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".") + " ", plural[3], " guessed with uncertainty. Use mo_uncertainties() to review ", plural[2], ".") warning(red(msg), call. = FALSE, immediate. = TRUE) # thus will always be shown, even if >= warnings diff --git a/R/zzz.R b/R/zzz.R index f0323055..8a2347e0 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -49,23 +49,27 @@ #' @importFrom data.table as.data.table setkey #' @importFrom dplyr %>% mutate case_when make_DT <- function() { - microorganismsDT <- as.data.table(AMR::microorganisms %>% - mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1, - kingdom == "Fungi" ~ 2, - kingdom == "Protozoa" ~ 3, - kingdom == "Archaea" ~ 4, - TRUE ~ 99), - # for fullname_lower: keep only dots, letters, - # numbers, slashes, spaces and dashes - fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", - # use this paste instead of `fullname` to - # work with Viridans Group Streptococci, etc. - tolower(trimws(paste(genus, species, subspecies)))))) + microorganismsDT <- AMR::microorganisms %>% + mutate(kingdom_index = case_when(kingdom == "Bacteria" ~ 1, + kingdom == "Fungi" ~ 2, + kingdom == "Protozoa" ~ 3, + kingdom == "Archaea" ~ 4, + TRUE ~ 99), + # for fullname_lower: keep only dots, letters, + # numbers, slashes, spaces and dashes + fullname_lower = gsub("[^.a-z0-9/ \\-]+", "", + # use this paste instead of `fullname` to + # work with Viridans Group Streptococci, etc. + tolower(trimws(ifelse(genus == "", + fullname, + paste(genus, species, subspecies)))))) %>% + as.data.table() + # so arrange data on prevalence first, then kingdom, then full name setkey(microorganismsDT, prevalence, kingdom_index, - fullname) + fullname_lower) microorganismsDT } diff --git a/docs/404.html b/docs/404.html index 7bdaaa2a..f98b3192 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 858b9650..ab0c5143 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 diff --git a/docs/articles/index.html b/docs/articles/index.html index aedec170..309c4158 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 diff --git a/docs/authors.html b/docs/authors.html index b2ef68f7..a256fc58 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 diff --git a/docs/index.html b/docs/index.html index 01f2d259..7e0c75e4 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 diff --git a/docs/news/index.html b/docs/news/index.html index 33f7bacf..71eaf50d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9031 + 0.8.0.9032 @@ -231,9 +231,9 @@ -
+

-AMR 0.8.0.9031 Unreleased +AMR 0.8.0.9032 Unreleased

Last updated: 15-Nov-2019

@@ -286,7 +286,7 @@ 
as.mo(c("Stafylococcus aureus",
         "staphylokok aureuz"))
 #> Warning: 
-#> Results of two values was guessed with uncertainty. Use mo_uncertainties() to review them.
+#> Results of two values were guessed with uncertainty. Use mo_uncertainties() to review them.
 #> Class 'mo'
 #> [1] B_STPHY_AURS B_STPHY_AURS
 
@@ -1385,7 +1385,7 @@ Using as.mo(..., allow_uncertain = 3)
       
Contents

       
    
-        
  • 0.8.0.9031
    • 
+        
  • 0.8.0.9032
    • 
         
  • 0.8.0
    • 
         
  • 0.7.1
    • 
         
  • 0.7.0
    • 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 12a663db..db35b2b9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -84,7 +84,7 @@
       
       
         AMR (for R)
-        0.8.0.9031
+        0.8.0.9032