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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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dr. M.S. (Matthijs) Berends
2021-08-16 21:54:34 +02:00
parent 4e1efd902c
commit a2d249962f
248 changed files with 2377 additions and 12201 deletions
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192
man/AMR-deprecated.Rd
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@ -3,201 +3,9 @@
\name{AMR-deprecated}
\alias{AMR-deprecated}
\alias{p_symbol}
\alias{filter_first_weighted_isolate}
\alias{key_antibiotics}
\alias{key_antibiotics_equal}
\alias{filter_ab_class}
\alias{filter_aminoglycosides}
\alias{filter_betalactams}
\alias{filter_carbapenems}
\alias{filter_cephalosporins}
\alias{filter_1st_cephalosporins}
\alias{filter_2nd_cephalosporins}
\alias{filter_3rd_cephalosporins}
\alias{filter_4th_cephalosporins}
\alias{filter_5th_cephalosporins}
\alias{filter_fluoroquinolones}
\alias{filter_glycopeptides}
\alias{filter_macrolides}
\alias{filter_oxazolidinones}
\alias{filter_penicillins}
\alias{filter_tetracyclines}
\title{Deprecated Functions}
\usage{
p_symbol(p, emptychar = " ")
filter_first_weighted_isolate(
x = NULL,
col_date = NULL,
col_patient_id = NULL,
col_mo = NULL,
...
)
key_antibiotics(
x = NULL,
col_mo = NULL,
universal_1 = guess_ab_col(x, "amoxicillin"),
universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
universal_3 = guess_ab_col(x, "cefuroxime"),
universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
universal_5 = guess_ab_col(x, "ciprofloxacin"),
universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
GramPos_1 = guess_ab_col(x, "vancomycin"),
GramPos_2 = guess_ab_col(x, "teicoplanin"),
GramPos_3 = guess_ab_col(x, "tetracycline"),
GramPos_4 = guess_ab_col(x, "erythromycin"),
GramPos_5 = guess_ab_col(x, "oxacillin"),
GramPos_6 = guess_ab_col(x, "rifampin"),
GramNeg_1 = guess_ab_col(x, "gentamicin"),
GramNeg_2 = guess_ab_col(x, "tobramycin"),
GramNeg_3 = guess_ab_col(x, "colistin"),
GramNeg_4 = guess_ab_col(x, "cefotaxime"),
GramNeg_5 = guess_ab_col(x, "ceftazidime"),
GramNeg_6 = guess_ab_col(x, "meropenem"),
warnings = TRUE,
...
)
key_antibiotics_equal(
y,
z,
type = "keyantimicrobials",
ignore_I = TRUE,
points_threshold = 2,
info = FALSE,
na.rm = TRUE,
...
)
filter_ab_class(
x,
ab_class,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_aminoglycosides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_betalactams(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_carbapenems(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_1st_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_2nd_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_3rd_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_4th_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_5th_cephalosporins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_fluoroquinolones(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_glycopeptides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_macrolides(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_oxazolidinones(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_penicillins(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_tetracyclines(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
}
\description{
These functions are so-called '\link{Deprecated}'. \strong{They will be removed in a future release.} Using the functions will give a warning with the name of the function it has been replaced by (if there is one).