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unit tests

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dr. M.S. (Matthijs) Berends
2023-01-30 17:24:03 +01:00
parent 89a577805f
commit 4b133d4c96
6 changed files with 57 additions and 16 deletions
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6
R/aa_helper_functions.R
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@ -722,9 +722,9 @@ format_class <- function(class, plural = FALSE) {
class <- "input created with `custom_eucast_rules()`"
}
if (any(c("mo", "ab", "sir") %in% class)) {
class <- paste0("of class <", class[1L], ">")
class <- paste0("of class '", class[1L], "'")
}
class[class == class.bak] <- paste0("of class <", class[class == class.bak], ">")
class[class == class.bak] <- paste0("of class '", class[class == class.bak], "'")
# output
vector_or(class, quotes = FALSE, sort = FALSE)
}
@ -854,7 +854,7 @@ meet_criteria <- function(object,
}
), na.rm = TRUE),
"the data provided in argument `", obj_name,
"` must contain at least one column of class <", contains_column_class, ">. ",
"` must contain at least one column of class '", contains_column_class, "'. ",
"See ?as.", contains_column_class, ".",
call = call_depth
)

28
R/mo.R
View File

@ -800,25 +800,31 @@ print.mo_uncertainties <- function(x, ...) {
return(invisible(NULL))
}
add_MO_lookup_to_AMR_env()
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
add_MO_lookup_to_AMR_env()
col_red <- function(x) font_rose_bg(font_black(x, collapse = NULL), collapse = NULL)
col_orange <- function(x) font_orange_bg(font_black(x, collapse = NULL), collapse = NULL)
col_yellow <- function(x) font_yellow_bg(font_black(x, collapse = NULL), collapse = NULL)
col_green <- function(x) font_green_bg(font_black(x, collapse = NULL), collapse = NULL)
if (has_colour()) {
cat(word_wrap("Colour keys: ",
font_red_bg(" 0.000-0.499 "),
font_orange_bg(" 0.500-0.599 "),
font_yellow_bg(" 0.600-0.699 "),
font_green_bg(" 0.700-1.000"),
col_red(" 0.000-0.499 "),
col_orange(" 0.500-0.599 "),
col_yellow(" 0.600-0.699 "),
col_green(" 0.700-1.000"),
add_fn = font_blue
), font_green_bg(" "), "\n", sep = "")
}
score_set_colour <- function(text, scores) {
# set colours to scores
text[scores >= 0.7] <- font_green_bg(text[scores >= 0.7], collapse = NULL)
text[scores >= 0.6 & scores < 0.7] <- font_yellow_bg(text[scores >= 0.6 & scores < 0.7], collapse = NULL)
text[scores >= 0.5 & scores < 0.6] <- font_orange_bg(text[scores >= 0.5 & scores < 0.6], collapse = NULL)
text[scores < 0.5] <- font_red_bg(text[scores < 0.5], collapse = NULL)
text[scores >= 0.7] <- col_green(text[scores >= 0.7])
text[scores >= 0.6 & scores < 0.7] <- col_yellow(text[scores >= 0.6 & scores < 0.7])
text[scores >= 0.5 & scores < 0.6] <- col_orange(text[scores >= 0.5 & scores < 0.6])
text[scores < 0.5] <- col_red(text[scores < 0.5])
text
}