diff --git a/DESCRIPTION b/DESCRIPTION index 24a28dfac..ee3d1f8ab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.7.1.9007 +Version: 0.7.1.9008 Date: 2019-07-04 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index a0dd0e324..0bb14c24d 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9007 +# AMR 0.7.1.9008 ### New * Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for `portion_*` functions or `count_*` functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter `only_all_tested` (**which defaults to `FALSE`**) replaces the old `also_single_tested` and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the `portion` and `count` help pages), where the %SI is being determined: @@ -39,6 +39,8 @@ * Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore * Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country * Fix for frequency tables when creating one directly on a group (using `group_by()`) +* The name of `RIF` is now Rifampicin instead of Rifampin +* The `antibiotics` data set is now sorted by name # AMR 0.7.1 diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 31e56183e..b6b7835f8 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -289,6 +289,8 @@ antibiotics <- filter(antibiotics, ab != "MOX") antibiotics <- filter(antibiotics, ab != "RFP") antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP" antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp")) +# Rifampicin is better known as a drug than Rifampin (Rifampin is still listed as a brand name), so: +antibiotics[which(antibiotics$ab == "RIF"), "name"] <- "Rifampicin" # PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so: antibiotics <- filter(antibiotics, ab != "PME") antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME" @@ -300,8 +302,9 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl")) antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct")) +antibiotics <- antibiotics %>% arrange(name) + class(antibiotics$ab) <- "ab" -class(antibiotics$atc) <- "atc" dim(antibiotics) # for R/data.R usethis::use_data(antibiotics, overwrite = TRUE) diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 8ecf8c515..82025b425 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 2a58abe8b..cf0c354f1 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9007 + 0.7.1.9008 diff --git a/docs/articles/index.html b/docs/articles/index.html index 4a1d63443..a13d0919d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9007 + 0.7.1.9008 diff --git a/docs/authors.html b/docs/authors.html index 4aa8c317c..cf84b4a77 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9007 + 0.7.1.9008 diff --git a/docs/index.html b/docs/index.html index 1ce0adff8..ebd8cd116 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.7.1.9007 + 0.7.1.9008 diff --git a/docs/news/index.html b/docs/news/index.html index a3303e19a..b2a19f2e7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9007 + 0.7.1.9008 @@ -232,9 +232,9 @@ -
+

-AMR 0.7.1.9007 Unreleased +AMR 0.7.1.9008 Unreleased

@@ -282,6 +282,8 @@
  • Fix for using mo_* functions where the coercion uncertainties and failures would not be available through mo_uncertainties() and mo_failures() anymore
  • Deprecated the country parameter of mdro() in favour of the already existing guideline parameter to support multiple guidelines within one country
  • Fix for frequency tables when creating one directly on a group (using group_by())
    • +
  • The name of RIF is now Rifampicin instead of Rifampin
    • +
  • The antibiotics data set is now sorted by name

    • @@ -1194,7 +1196,7 @@ Using as.mo(..., allow_uncertain = 3)

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