diff --git a/.gitignore b/.gitignore
index 28ba0c21..e2371544 100755
--- a/.gitignore
+++ b/.gitignore
@@ -20,3 +20,4 @@ vignettes/*.R
^CRAN-RELEASE$
packrat/lib*/
packrat/src/
+cran-comments.md
diff --git a/DESCRIPTION b/DESCRIPTION
index 58450c56..32556885 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 0.6.1.9046
+Version: 0.6.1.9047
Date: 2019-05-31
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/R/zzz.R b/R/zzz.R
index 9ccbe71c..9e4f5c87 100755
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -29,10 +29,6 @@
microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
setkey(microorganisms.oldDT, col_id, fullname)
- assign(x = "microorganisms",
- value = make(),
- envir = asNamespace("AMR"))
-
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
@@ -55,44 +51,9 @@
}
-#' @importFrom dplyr mutate case_when
-make <- function() {
- AMR::microorganisms %>%
- mutate(prevalence = case_when(
- class == "Gammaproteobacteria"
- | genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
- | mo == "UNKNOWN"
- ~ 1,
- phylum %in% c("Proteobacteria",
- "Firmicutes",
- "Actinobacteria",
- "Sarcomastigophora")
- | genus %in% c("Aspergillus",
- "Bacteroides",
- "Candida",
- "Capnocytophaga",
- "Chryseobacterium",
- "Cryptococcus",
- "Elisabethkingia",
- "Flavobacterium",
- "Fusobacterium",
- "Giardia",
- "Leptotrichia",
- "Mycoplasma",
- "Prevotella",
- "Rhodotorula",
- "Treponema",
- "Trichophyton",
- "Ureaplasma")
- | rank %in% c("kingdom", "phylum", "class", "order", "family")
- ~ 2,
- TRUE ~ 3
- ))
-}
-
#' @importFrom data.table as.data.table setkey
make_DT <- function() {
- microorganismsDT <- as.data.table(make())
+ microorganismsDT <- as.data.table(AMR::microorganisms)
microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
setkey(microorganismsDT,
prevalence,
diff --git a/data/microorganisms.rda b/data/microorganisms.rda
index 9b828512..a38d14b7 100755
Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index a0ef0fc6..1e2b543f 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9f01235f..a375e6b7 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
diff --git a/docs/authors.html b/docs/authors.html
index 23a5a4b6..59f824a0 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
diff --git a/docs/index.html b/docs/index.html
index 7df35705..27ab88fd 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
diff --git a/docs/news/index.html b/docs/news/index.html
index afd0e54e..e4adec12 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
diff --git a/docs/reference/ggplot_rsi.html b/docs/reference/ggplot_rsi.html
index 04d99d0f..f316a1e5 100644
--- a/docs/reference/ggplot_rsi.html
+++ b/docs/reference/ggplot_rsi.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9046
+ 0.6.1.9047
@@ -485,7 +485,7 @@
nrow = 1,
title = "AMR of Top Three Microorganisms In Blood Culture Isolates",
subtitle = expression(paste("Only First Isolates, CoNS grouped according to Becker ", italic("et al."), " (2014)")),
- x.title = "Antibiotic (Ears-Net code)")
+ x.title = "Antibiotic (EARS-Net code)")
# }
diff --git a/reproduction_of_microorganisms.R b/reproduction_of_microorganisms.R
index ba2e899c..f2eb82d0 100644
--- a/reproduction_of_microorganisms.R
+++ b/reproduction_of_microorganisms.R
@@ -452,6 +452,39 @@ MOs <- MOs %>%
sum(duplicated(MOs$mo))
colnames(MOs)
+# set prevalence per species
+MOs <- MOs %>%
+ mutate(prevalence = case_when(
+ class == "Gammaproteobacteria"
+ | genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
+ | mo == "UNKNOWN"
+ ~ 1,
+ phylum %in% c("Proteobacteria",
+ "Firmicutes",
+ "Actinobacteria",
+ "Sarcomastigophora")
+ | genus %in% c("Aspergillus",
+ "Bacteroides",
+ "Candida",
+ "Capnocytophaga",
+ "Chryseobacterium",
+ "Cryptococcus",
+ "Elisabethkingia",
+ "Flavobacterium",
+ "Fusobacterium",
+ "Giardia",
+ "Leptotrichia",
+ "Mycoplasma",
+ "Prevotella",
+ "Rhodotorula",
+ "Treponema",
+ "Trichophyton",
+ "Ureaplasma")
+ | rank %in% c("kingdom", "phylum", "class", "order", "family")
+ ~ 2,
+ TRUE ~ 3
+ ))
+
# save it
MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R
index 27465fc9..979d5f31 100644
--- a/tests/testthat/test-ggplot_rsi.R
+++ b/tests/testthat/test-ggplot_rsi.R
@@ -59,9 +59,6 @@ test_that("ggplot_rsi works", {
summarise_all(count_IR) %>% as.double()
)
- expect_equal(colnames(getlbls(septic_patients %>% select(AMC, CIP))),
- c("Interpretation", "Antibiotic", "Value", "lbl"))
-
expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
expect_error(geom_rsi(septic_patients, fun = "invalid"))