diff --git a/DESCRIPTION b/DESCRIPTION
index 4fb8a474..5a0ed1ae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
Version: 1.3.0
-Date: 2020-07-29
+Date: 2020-07-30
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
diff --git a/R/mic.R b/R/mic.R
index 32c64ad4..1243e89c 100755
--- a/R/mic.R
+++ b/R/mic.R
@@ -71,8 +71,8 @@ as.mic <- function(x, na.rm = FALSE) {
# transform => to >= and =< to <=
x <- gsub("=<", "<=", x, fixed = TRUE)
x <- gsub("=>", ">=", x, fixed = TRUE)
- # starting dots must start with 0
- x <- gsub("^[.]+", "0.", x)
+ # dots without a leading zero must start with 0
+ x <- gsub("([^0-9]|^)[.]", "\\10.", x)
# values like "<=0.2560.512" should be 0.512
x <- gsub(".*[.].*[.]", "0.", x)
# remove ending .0
diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html
index f6101862..aa04f346 100644
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.2.0.9037
+ 1.3.0
@@ -186,7 +186,7 @@
How to conduct AMR analysis
Matthijs S. Berends
- 24 July 2020
+ 30 July 2020
Source: vignettes/AMR.Rmd
AMR.Rmd
@@ -195,7 +195,7 @@
-Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 24 July 2020.
+Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 30 July 2020.
Introduction
@@ -226,21 +226,21 @@
-| 2020-07-24 |
+2020-07-30 |
abcd |
Escherichia coli |
S |
S |
-| 2020-07-24 |
+2020-07-30 |
abcd |
Escherichia coli |
S |
R |
-| 2020-07-24 |
+2020-07-30 |
efgh |
Escherichia coli |
R |
@@ -336,68 +336,68 @@
-| 2014-06-04 |
-V5 |
+2017-06-10 |
+J6 |
Hospital B |
Escherichia coli |
+I |
R |
S |
S |
+M |
+
+
+| 2013-08-26 |
+H10 |
+Hospital A |
+Escherichia coli |
+S |
+S |
+R |
+S |
+M |
+
+
+| 2016-02-09 |
+S7 |
+Hospital D |
+Escherichia coli |
+R |
+S |
+R |
S |
F |
-| 2015-09-20 |
-M6 |
-Hospital A |
+2013-06-27 |
+A5 |
+Hospital B |
Escherichia coli |
-R |
+S |
S |
S |
S |
M |
-| 2017-05-14 |
-Q6 |
-Hospital C |
-Streptococcus pneumoniae |
-R |
-S |
-S |
-S |
-F |
-
-
-| 2017-03-12 |
-O3 |
+2017-03-03 |
+Q4 |
Hospital D |
-Klebsiella pneumoniae |
-S |
-R |
-S |
-S |
-F |
-
-
-| 2017-12-27 |
-P8 |
-Hospital B |
Escherichia coli |
-S |
+R |
S |
S |
S |
F |
-| 2013-11-30 |
-B10 |
-Hospital B |
+2015-07-13 |
+I5 |
+Hospital A |
Staphylococcus aureus |
-I |
S |
S |
+R |
S |
M |
@@ -432,16 +432,16 @@ Longest: 1
| 1 |
M |
-10,487 |
-52.44% |
-10,487 |
-52.44% |
+10,312 |
+51.56% |
+10,312 |
+51.56% |
| 2 |
F |
-9,513 |
-47.57% |
+9,688 |
+48.44% |
20,000 |
100.00% |
@@ -481,7 +481,7 @@ Longest: 1
# NOTE: Using column `bacteria` as input for `col_mo`.
# NOTE: Using column `date` as input for `col_date`.
# NOTE: Using column `patient_id` as input for `col_patient_id`.