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use dplyr where available, new antibiogram()
for WISCA, fixed Salmonella Typhi/Paratyphi
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@ -202,7 +202,7 @@ ggplot_sir <- function(data,
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meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
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language <- validate_language(language)
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meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
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meet_criteria(colours, allow_class = c("character", "logical"))
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@ -300,7 +300,7 @@ geom_sir <- function(position = NULL,
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meet_criteria(x, allow_class = "character", has_length = 1)
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meet_criteria(fill, allow_class = "character", has_length = 1)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
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language <- validate_language(language)
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meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
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@ -486,7 +486,7 @@ labels_sir_count <- function(position = NULL,
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meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
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meet_criteria(x, allow_class = "character", has_length = 1)
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meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE)
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meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
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language <- validate_language(language)
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meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
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meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
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@ -519,11 +519,11 @@ labels_sir_count <- function(position = NULL,
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language = language
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)
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transformed$gr <- transformed[, x_name, drop = TRUE]
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transformed %pm>%
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pm_group_by(gr) %pm>%
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pm_mutate(lbl = paste0("n=", isolates)) %pm>%
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pm_ungroup() %pm>%
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pm_select(-gr)
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transformed %>%
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group_by(gr) %>%
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mutate(lbl = paste0("n=", isolates)) %>%
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ungroup() %>%
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select(-gr)
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}
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)
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}
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