diff --git a/DESCRIPTION b/DESCRIPTION index 743ec28a..3761533c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9032 +Version: 1.7.1.9033 Date: 2021-08-30 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 61be7e96..5fe02526 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9032 +# `AMR` 1.7.1.9033 ## Last updated: 30 August 2021 ### Breaking changes diff --git a/R/first_isolate.R b/R/first_isolate.R index ca4e6cb7..39440fb6 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -25,7 +25,7 @@ #' Determine First Isolates #' -#' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports [grouping with the `dplyr` package][dplyr::group_by()] . +#' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package. #' @inheritSection lifecycle Stable Lifecycle #' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*. #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index f734ce90..727d4bf2 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R index 6e9fcc6f..fa57d708 100644 --- a/data-raw/_install_deps.R +++ b/data-raw/_install_deps.R @@ -24,13 +24,13 @@ # ==================================================================== # # some old R instances have trouble installing tinytest, so we ship it too -install.packages("data-raw/tinytest_1.2.4.10.tar.gz", dependencies = c("Depends", "Imports")) +install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports")) install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(unlist(packageDescription("AMR", fields = c("Suggests", "Enhances"))), - ", ?"))) + split = ", ?"))) cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n") to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] diff --git a/data-raw/tinytest_1.3.1.tar.gz b/data-raw/tinytest_1.3.1.tar.gz new file mode 100644 index 00000000..e8729b32 Binary files /dev/null and b/data-raw/tinytest_1.3.1.tar.gz differ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index e7f642ac..fa2c7daf 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9030 + 1.7.1.9033 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 69ddc1fa..69d1b88e 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9032 + 1.7.1.9033 diff --git a/docs/authors.html b/docs/authors.html index efbc0dd5..c753fc1c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9030 + 1.7.1.9033 @@ -241,7 +241,7 @@

Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with -Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4

+Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.

@Article{,
   title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
   author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
@@ -251,6 +251,16 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
   year = {2021},
   url = {https://www.biorxiv.org/content/10.1101/810622v4},
 }
+

Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131.

+ 
@PhdThesis{,
+  title = {A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis},
+  author = {M S Berends},
+  publisher = {University of Groningen},
+  school = {University of Groningen},
+  doi = {10.33612/diss.177417131},
+  pages = {288},
+  year = {2021},
+}

Authors

diff --git a/docs/index.html b/docs/index.html index 3c05d5d3..f2046e54 100644 --- a/docs/index.html +++ b/docs/index.html @@ -47,7 +47,7 @@ AMR (for R) - 1.7.1.9030 + 1.7.1.9033
diff --git a/docs/news/index.html b/docs/news/index.html index d58b78b1..d71668d4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9032 + 1.7.1.9033 @@ -240,9 +240,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9032

+
+

+ Unreleased AMR 1.7.1.9033

Last updated: 30 August 2021 diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index a3f9824d..837be5df 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -50,7 +50,7 @@ +). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package." /> @@ -94,7 +94,7 @@ AMR (for R) - 1.7.1.9031 + 1.7.1.9033

@@ -245,7 +245,7 @@

Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864 -). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package .

+). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package.

first_isolate(
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 0fb823ab..a46b97f8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -92,7 +92,7 @@
       
       
         AMR (for R)
-        1.7.1.9031
+        1.7.1.9033
diff --git a/docs/survey.html b/docs/survey.html index 50851392..f1bfc11f 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9030 + 1.7.1.9033
diff --git a/index.md b/index.md index 6e6b3d79..819a50c0 100644 --- a/index.md +++ b/index.md @@ -1,7 +1,6 @@ # `AMR` (for R) -> This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. -> Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131). +> This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131). ### What is `AMR` (for R)? diff --git a/inst/CITATION b/inst/CITATION index 14f263d5..63e5f811 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,4 +1,4 @@ -citHeader("To cite our AMR package in publications, please use (for now):") +citHeader("To cite our AMR package in publications, please use below preprint. This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!") citEntry( entry = "Article", @@ -10,7 +10,16 @@ citEntry( year = 2021, url = "https://www.biorxiv.org/content/10.1101/810622v4", textVersion = "Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with -Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4" -) +Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.") -citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!") +citEntry( + entry = "PhdThesis", + title = "A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis", + author = "M S Berends", + publisher = "University of Groningen", + school = "University of Groningen", + doi = "10.33612/diss.177417131", + pages = 288, + year = 2021, + textVersion = "Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131." +) diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 0e305900..90f577bb 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -90,7 +90,7 @@ filter_first_isolate( A \code{\link{logical}} vector } \description{ -Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports \link[dplyr:group_by]{grouping with the \code{dplyr} package} . +Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package. } \details{ To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.