From 8a66e475d77b775aa22cc85f4ba84d07466d1b34 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Mon, 22 Jun 2020 13:18:40 +0200 Subject: [PATCH] (v1.2.0.9013) unit test fix --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/rsi.R | 2 ++ docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 8 ++++---- docs/pkgdown.yml | 2 +- docs/reference/as.rsi.html | 6 ++++-- docs/reference/index.html | 2 +- man/as.rsi.Rd | 2 ++ tests/testthat/test-rsi.R | 10 ++++------ 14 files changed, 25 insertions(+), 21 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff70b6dd..e5a0937b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9012 +Version: 1.2.0.9013 Date: 2020-06-22 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index a80f9837..c3daabc8 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9012 +# AMR 1.2.0.9013 ## Last updated: 22-Jun-2020 ### New diff --git a/R/rsi.R b/R/rsi.R index 6bfb70b1..16050fc5 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -59,6 +59,8 @@ #' @seealso [as.mic()] #' @inheritSection AMR Read more on our website! #' @examples +#' summary(example_isolates) # see all R/SI results at a glance +#' #' # For INTERPRETING disk diffusion and MIC values ----------------------- #' #' # a whole data set, even with combined MIC values and disk zones diff --git a/docs/404.html b/docs/404.html index 15b5a2e4..0a28af01 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 10613673..5887367b 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 diff --git a/docs/articles/index.html b/docs/articles/index.html index 7c39a51e..d5bd305a 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 diff --git a/docs/authors.html b/docs/authors.html index 4b6b8751..d89dfd3c 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 diff --git a/docs/index.html b/docs/index.html index bc23ff66..7e872990 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 diff --git a/docs/news/index.html b/docs/news/index.html index 165231ff..88cd6c66 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9012 + 1.2.0.9013 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.2.0.9012 Unreleased +
+

+AMR 1.2.0.9013 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 53308601..31d91fe1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-06-22T10:13Z +last_built: 2020-06-22T11:18Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/as.rsi.html b/docs/reference/as.rsi.html index 7daad110..18b4879e 100644 --- a/docs/reference/as.rsi.html +++ b/docs/reference/as.rsi.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0 + 1.2.0.9013

@@ -342,7 +342,9 @@ The lifecycle of this function is stable

as.mic()

Examples

- 
# For INTERPRETING disk diffusion and MIC values -----------------------
+    
summary(example_isolates) # see all R/SI results at a glance
+
+# For INTERPRETING disk diffusion and MIC values -----------------------
 
 # a whole data set, even with combined MIC values and disk zones
 df <- data.frame(microorganism = "E. coli",
diff --git a/docs/reference/index.html b/docs/reference/index.html
index ca96a488..fb04aa9c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
       
       
         AMR (for R)
-        1.2.0.9012
+        1.2.0.9013

diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index a62d9ec8..ddfec9ee 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -99,6 +99,8 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https:// } \examples{ +summary(example_isolates) # see all R/SI results at a glance + # For INTERPRETING disk diffusion and MIC values ----------------------- # a whole data set, even with combined MIC values and disk zones diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R index f55a7ff3..ac6b00ba 100644 --- a/tests/testthat/test-rsi.R +++ b/tests/testthat/test-rsi.R @@ -27,7 +27,6 @@ test_that("rsi works", { expect_true(as.rsi("S") < as.rsi("I")) expect_true(as.rsi("I") < as.rsi("R")) - expect_true(as.rsi("R") > as.rsi("S")) expect_true(is.rsi(as.rsi("S"))) # print plots, should not raise errors @@ -40,11 +39,10 @@ test_that("rsi works", { expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA) expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi", - "" = "0", - "Sum S" = "1", - "Sum IR" = "1", - "-Sum R" = "1", - "-Sum I" = "0")) + "%R" = "50% (n=1)", + "%SI" = "50% (n=1)", + "- %S" = "50% (n=1)", + "- %I" = "0% (n=0)")) expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)), rep(FALSE, length(example_isolates)))