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(v2.1.1.9155) new mic_p50() and mic_p90() - updated AMR intro

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dr. M.S. (Matthijs) Berends
2025-02-23 11:18:08 +01:00
parent 226d10f546
commit aa8f6af185
24 changed files with 481 additions and 99 deletions
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39
R/antibiogram.R
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@ -923,19 +923,16 @@ antibiogram.default <- function(x,
}
}
out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
out <- structure(as_original_data_class(new_df, class(x), extra_class = "antibiogram"),
has_syndromic_group = has_syndromic_group,
combine_SI = combine_SI,
wisca = wisca,
conf_interval = conf_interval,
formatting_type = formatting_type,
wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
long_numeric = as_original_data_class(long_numeric, class(x)))
rownames(out) <- NULL
rownames(wisca_parameters) <- NULL
rownames(long_numeric) <- NULL
structure(out,
has_syndromic_group = has_syndromic_group,
combine_SI = combine_SI,
wisca = wisca,
conf_interval = conf_interval,
formatting_type = formatting_type,
wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
long_numeric = as_original_data_class(long_numeric, class(x))
)
out
}
#' @method antibiogram grouped_df
@ -1041,14 +1038,16 @@ antibiogram.grouped_df <- function(x,
close(progress)
structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
has_syndromic_group = FALSE,
combine_SI = isTRUE(combine_SI),
wisca = isTRUE(wisca),
conf_interval = conf_interval,
formatting_type = formatting_type,
wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
long_numeric = as_original_data_class(long_numeric, class(x)))
out <- structure(as_original_data_class(out, class(x), extra_class = "antibiogram"),
has_syndromic_group = FALSE,
combine_SI = isTRUE(combine_SI),
wisca = isTRUE(wisca),
conf_interval = conf_interval,
formatting_type = formatting_type,
wisca_parameters = as_original_data_class(wisca_parameters, class(x)),
long_numeric = as_original_data_class(long_numeric, class(x)))
rownames(out) <- NULL
out
}
#' @export