diff --git a/.Rbuildignore b/.Rbuildignore index 2d3998c0..45a4d842 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -23,3 +23,5 @@ ^data-raw$ R/aa_test.R$ ^\.lintr$ +^vignettes/benchmark.* +^vignettes/SPSS.* diff --git a/DESCRIPTION b/DESCRIPTION index fe68fb63..5a37840c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.7.1.9106 -Date: 2019-10-13 +Version: 0.7.1.9107 +Date: 2019-10-15 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), @@ -29,7 +29,9 @@ Authors@R: c( family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl")) Description: Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by - using evidence-based methods. + using evidence-based methods, like those defined by Leclercq et al. (2013) + and the Clinical and Laboratory + Standards Institute (2014) . Depends: R (>= 3.1.0) Imports: diff --git a/NEWS.md b/NEWS.md index f60f7e3a..619edfe4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,5 @@ -# AMR 0.7.1.9106 -Last updated: 13-Oct-2019 - +# AMR 0.7.1.9107 +Last updated: 15-Oct-2019 ### Breaking * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: ```r diff --git a/R/atc_online.R b/R/atc_online.R index cb422c01..04ca0a2c 100644 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -167,7 +167,7 @@ atc_online_property <- function(atc_code, returnvalue[i] <- NA next } else { - for (j in seq_len(length(tbl))) { + for (j in seq_len(nrow(tbl))) { if (tbl[j, "adm.r"] == administration) { returnvalue[i] <- tbl[j, property] } diff --git a/docs/404.html b/docs/404.html index e2f8bc00..ddedb2ac 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9106 + 0.7.1.9107 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 73c396f4..768a238d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9106 + 0.7.1.9107 diff --git a/docs/articles/index.html b/docs/articles/index.html index b277fe98..b6858dc1 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9106 + 0.7.1.9107 diff --git a/docs/authors.html b/docs/authors.html index c67b5b88..1f5f1a2c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9106 + 0.7.1.9107 diff --git a/docs/index.html b/docs/index.html index 4590db85..cb38fd10 100644 --- a/docs/index.html +++ b/docs/index.html @@ -22,7 +22,9 @@ + using evidence-based methods, like those defined by Leclercq et al. (2013) + <doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory + Standards Institute (2014) <isbn: 1-56238-899-1>.">