diff --git a/DESCRIPTION b/DESCRIPTION index 8097d6e5..a899b173 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.7.1.9077 +Version: 0.7.1.9078 Date: 2019-09-20 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 35028efd..d5ce2e45 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9077 +# AMR 0.7.1.9078 Last updated: 20-Sep-2019 ### Breaking diff --git a/R/mo.R b/R/mo.R index fc2f2642..222caa16 100755 --- a/R/mo.R +++ b/R/mo.R @@ -1539,7 +1539,8 @@ exec_as.mo <- function(x, # THEN TRY PREVALENT IN HUMAN INFECTIONS ---- x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2], - data.old_to_check = microorganisms.oldDT[prevalence == 2], + data.old_to_check = microorganisms.oldDT[prevalence %in% c(2, 3)], # run all other old MOs the second time, + # otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly a.x_backup = x_backup[i], b.x_trimmed = x_trimmed[i], c.x_trimmed_without_group = x_trimmed_without_group[i], @@ -1558,7 +1559,7 @@ exec_as.mo <- function(x, # THEN UNPREVALENT IN HUMAN INFECTIONS ---- x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 3], - data.old_to_check = microorganisms.oldDT[prevalence == 3], + data.old_to_check = microorganisms.oldDT[prevalence == 999], a.x_backup = x_backup[i], b.x_trimmed = x_trimmed[i], c.x_trimmed_without_group = x_trimmed_without_group[i], diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 407b1ee8..5a5d8f45 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@
diff --git a/docs/articles/index.html b/docs/articles/index.html index 138cf7c6..deda88cf 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ diff --git a/docs/authors.html b/docs/authors.html index e4b1ecbb..237e888f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ diff --git a/docs/index.html b/docs/index.html index 54f22dcb..8a42b888 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 8f3f8db0..4dcb1e4a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ @@ -225,9 +225,9 @@ -Last updated: 20-Sep-2019
as.mo(..., allow_uncertain = 3)
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