diff --git a/DESCRIPTION b/DESCRIPTION
index c0d327632..4aef11f40 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 0.6.1.9042
-Date: 2019-05-29
+Version: 0.6.1.9043
+Date: 2019-05-30
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(
diff --git a/R/age.R b/R/age.R
index 26dbaa2ac..bb9d4c102 100755
--- a/R/age.R
+++ b/R/age.R
@@ -107,7 +107,7 @@ age <- function(x, reference = Sys.Date()) {
#' # resistance of ciprofloxacine per age group
#' library(dplyr)
#' septic_patients %>%
-#' filter_first_isolate) %>%
+#' filter_first_isolate() %>%
#' filter(mo == as.mo("E. coli")) %>%
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group, CIP) %>%
diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R
index 126cb796b..d312a4db0 100755
--- a/R/ggplot_rsi.R
+++ b/R/ggplot_rsi.R
@@ -162,9 +162,9 @@ ggplot_rsi <- function(data,
language = get_locale(),
fun = count_df,
nrow = NULL,
- datalabels = TRUE,
+ datalabels = FALSE,
datalabels.size = 3,
- datalabels.colour = "grey15",
+ datalabels.colour = "white",
...) {
stopifnot_installed_package("ggplot2")
@@ -209,7 +209,7 @@ ggplot_rsi <- function(data,
position <- "fill"
}
if (fun_name == "portion_df"
- | (fun_name == "count_df" & position == "fill")) {
+ | (fun_name == "count_df" & identical(position, "fill"))) {
# portions, so use y scale with percentage
p <- p + scale_y_percent(breaks = breaks, limits = limits)
}
@@ -361,13 +361,13 @@ theme_rsi <- function() {
labels_rsi_count <- function(position = NULL,
x = "Antibiotic",
datalabels.size = 3,
- datalabels.colour = "grey15") {
+ datalabels.colour = "white") {
stopifnot_installed_package("ggplot2")
if (is.null(position)) {
position <- "fill"
}
- if (position == "fill") {
- position <- ggplot2::position_fill(vjust = 0.5)
+ if (identical(position, "fill")) {
+ position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
}
ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
x = x,
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index fde2caf98..9f20e05a7 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 6ff3241fe..94f10ec0f 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/docs/authors.html b/docs/authors.html
index 002b35ca1..8a1fd7592 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/docs/index.html b/docs/index.html
index 766ee6535..e0e6061f2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/docs/news/index.html b/docs/news/index.html
index fd7eb5472..75e59ab8f 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/docs/reference/age_groups.html b/docs/reference/age_groups.html
index 5e25dba68..336945a73 100644
--- a/docs/reference/age_groups.html
+++ b/docs/reference/age_groups.html
@@ -80,7 +80,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
@@ -291,38 +291,37 @@
Examples
- # NOT RUN {
-ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
+ # NOT RUN {
+ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
-# split into 0-49 and 50+
-age_groups(ages, 50)
+# split into 0-49 and 50+
+age_groups(ages, 50)
-# split into 0-19, 20-49 and 50+
-age_groups(ages, c(20, 50))
+# split into 0-19, 20-49 and 50+
+age_groups(ages, c(20, 50))
-# split into groups of ten years
-age_groups(ages, 1:10 * 10)
-age_groups(ages, split_at = "tens")
+# split into groups of ten years
+age_groups(ages, 1:10 * 10)
+age_groups(ages, split_at = "tens")
-# split into groups of five years
-age_groups(ages, 1:20 * 5)
-age_groups(ages, split_at = "fives")
+# split into groups of five years
+age_groups(ages, 1:20 * 5)
+age_groups(ages, split_at = "fives")
-# split specifically for children
-age_groups(ages, "children")
-# same:
-age_groups(ages, c(1, 2, 4, 6, 13, 17))
+# split specifically for children
+age_groups(ages, "children")
+# same:
+age_groups(ages, c(1, 2, 4, 6, 13, 17))
-# resistance of ciprofloxacine per age group
-library(dplyr)
-septic_patients %>%
- filter_first_isolate) %>%
- filter(mo == as.mo("E. coli")) %>%
- group_by(age_group = age_groups(age)) %>%
- select(age_group, CIP) %>%
- ggplot_rsi(x = "age_group")
-# }
-
+# resistance of ciprofloxacine per age group
+library(dplyr)
+septic_patients %>%
+ filter_first_isolate() %>%
+ filter(mo == as.mo("E. coli")) %>%
+ group_by(age_group = age_groups(age)) %>%
+ select(age_group, CIP) %>%
+ ggplot_rsi(x = "age_group")
+# }
@@ -252,8 +252,8 @@
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE,
combine_IR = FALSE, language = get_locale(), fun = count_df,
- nrow = NULL, datalabels = TRUE, datalabels.size = 3,
- datalabels.colour = "grey15", ...)
+ nrow = NULL, datalabels = FALSE, datalabels.size = 3,
+ datalabels.colour = "white", ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "name",
@@ -269,7 +269,7 @@
theme_rsi()
labels_rsi_count(position = NULL, x = "Antibiotic",
- datalabels.size = 3, datalabels.colour = "grey15")
+ datalabels.size = 3, datalabels.colour = "white")
Arguments
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a6b35ce79..48612a198 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -78,7 +78,7 @@
AMR (for R)
- 0.6.1.9042
+ 0.6.1.9043
diff --git a/git_premaster.sh b/git_premaster.sh
index 59c7315a7..8886a0fe5 100755
--- a/git_premaster.sh
+++ b/git_premaster.sh
@@ -55,7 +55,7 @@ echo "••••••••••••••••••••••••
echo "• Uploading to repository •"
echo "•••••••••••••••••••••••••••"
git add .
-git commit -a -m "$1" --quiet
+git commit -a -m "(v$new_version) $1" --quiet
git push --quiet
echo "Comparison:"
echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
diff --git a/man/age_groups.Rd b/man/age_groups.Rd
index cd0e51017..4186e44f5 100644
--- a/man/age_groups.Rd
+++ b/man/age_groups.Rd
@@ -61,7 +61,7 @@ age_groups(ages, c(1, 2, 4, 6, 13, 17))
# resistance of ciprofloxacine per age group
library(dplyr)
septic_patients \%>\%
- filter_first_isolate) \%>\%
+ filter_first_isolate() \%>\%
filter(mo == as.mo("E. coli")) \%>\%
group_by(age_group = age_groups(age)) \%>\%
select(age_group, CIP) \%>\%
diff --git a/man/ggplot_rsi.Rd b/man/ggplot_rsi.Rd
index a3f8549a3..1e49ba753 100644
--- a/man/ggplot_rsi.Rd
+++ b/man/ggplot_rsi.Rd
@@ -14,8 +14,8 @@ ggplot_rsi(data, position = NULL, x = "Antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE,
combine_IR = FALSE, language = get_locale(), fun = count_df,
- nrow = NULL, datalabels = TRUE, datalabels.size = 3,
- datalabels.colour = "grey15", ...)
+ nrow = NULL, datalabels = FALSE, datalabels.size = 3,
+ datalabels.colour = "white", ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
fill = "Interpretation", translate_ab = "name",
@@ -31,7 +31,7 @@ scale_rsi_colours()
theme_rsi()
labels_rsi_count(position = NULL, x = "Antibiotic",
- datalabels.size = 3, datalabels.colour = "grey15")
+ datalabels.size = 3, datalabels.colour = "white")
}
\arguments{
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}