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autoplot fix

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dr. M.S. (Matthijs) Berends 2024-05-30 16:39:59 +02:00
parent d4490c7f25
commit ba4dc20cf3
4 changed files with 11 additions and 10 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.1.1.9034 Version: 2.1.1.9035
Date: 2024-05-30 Date: 2024-05-30
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9034 # AMR 2.1.1.9035
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)* *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*

5
R/plot.R
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@ -760,9 +760,10 @@ autoplot.sir <- function(object,
} }
df <- as.data.frame(table(object), stringsAsFactors = TRUE) df <- as.data.frame(table(object), stringsAsFactors = TRUE)
colnames(df) <- c("sir", "count") colnames(df) <- c("x", "n")
df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "N")), , drop = FALSE]
ggplot2::ggplot(df) + ggplot2::ggplot(df) +
ggplot2::geom_col(ggplot2::aes(x = sir, y = count, fill = sir)) + ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511) # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual( ggplot2::scale_fill_manual(
values = c( values = c(

12
R/sir.R
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@ -907,15 +907,15 @@ as_sir_method <- function(method_short,
same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name) same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
same_ab.bak <- generalise_antibiotic_name(ab.bak) == generalise_antibiotic_name(agent_name) same_ab.bak <- generalise_antibiotic_name(ab.bak) == generalise_antibiotic_name(agent_name)
agent_formatted[same_ab.bak] <- paste0(agent_formatted[same_ab.bak], " (", ab, ")") agent_formatted[same_ab.bak] <- paste0(agent_formatted[same_ab.bak], " (", ab, ")")
agent_formatted[same_ab.bak & !same_ab] <- paste0(agent_formatted[same_ab.bak & !same_ab], agent_formatted[!same_ab.bak & !same_ab] <- paste0(agent_formatted[!same_ab.bak & !same_ab],
" (", ifelse(ab.bak[same_ab.bak & !same_ab] == ab[same_ab.bak & !same_ab], " (", ifelse(ab.bak[!same_ab.bak & !same_ab] == ab[!same_ab.bak & !same_ab],
"", "",
paste0(ab[same_ab.bak & !same_ab], ", ")), paste0(ab[!same_ab.bak & !same_ab], ", ")),
agent_name[same_ab.bak & !same_ab], agent_name[!same_ab.bak & !same_ab],
")") ")")
# this intro text will also be printed in the progress bar in the `progress` package is installed # this intro text will also be printed in the progress bar if the `progress` package is installed
intro_txt <- paste0("Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), intro_txt <- paste0("Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
ifelse(length(agent_formatted) == 1, agent_formatted, ""), ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), vector_and(ab, quotes = FALSE)),
mo_var_found, mo_var_found,
ifelse(identical(reference_data, AMR::clinical_breakpoints), ifelse(identical(reference_data, AMR::clinical_breakpoints),
paste0(", ", font_bold(guideline_coerced)), paste0(", ", font_bold(guideline_coerced)),