diff --git a/DESCRIPTION b/DESCRIPTION index 24a28dfa..ee3d1f8a 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 a0dd0e32..0bb14c24 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 31e56183..b6b7835f 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 8ecf8c51..82025b42 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 2a58abe8..cf0c354f 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 4a1d6344..a13d0919 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 4aa8c317..cf84b4a7 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 1ce0adff..ebd8cd11 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 a3303e19..b2a19f2e 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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