API for AMR
Antimicrobial Resistance Analysis

Global functions
%like% Man page
%like_case% Man page
.onLoad Source code
3MRGN Man page
4MRGN Man page
AMR Man page
AMR-deprecated Man page
ATC Man page
BRMO Man page
EUCAST Man page
MDR Man page
PDR Man page
WHOCC Man page
WHONET Man page
XDR Man page
`%>%` Source code
ab Man page
ab_atc Man page Source code
ab_atc_group1 Man page Source code
ab_atc_group2 Man page Source code
ab_cid Man page Source code
ab_ddd Man page Source code
ab_group Man page Source code
ab_info Man page Source code
ab_loinc Man page Source code
ab_name Man page Source code
ab_property Man page Source code
ab_synonyms Man page Source code
ab_tradenames Man page Source code
ab_url Man page Source code
ab_validate Source code
add_count Source code
add_tally Source code
addin_insert_in Source code
addin_insert_like Source code
age Man page Source code
age_groups Man page Source code
all_of Source code
all_valid_disks Source code
all_valid_mics Source code
anti_join Source code
anti_join_microorganisms Man page Source code
antibiotics Man page
antivirals Man page
any_of Source code
apply_grouped_function Source code
arrange Source code
arrange.default Source code
arrange.grouped_data Source code
as.ab Man page Source code
as.data.frame.ab Source code
as.data.frame.mo Source code
as.disk Man page Source code
as.double.mic Source code
as.integer.mic Source code
as.mic Man page Source code
as.mo Man page Source code
as.numeric.mic Source code
as.rsi Man page Source code
as.rsi.data.frame Man page Source code
as.rsi.default Source code
as.rsi.disk Man page Source code
as.rsi.mic Man page Source code
atc_online_ddd Man page Source code
atc_online_groups Man page Source code
atc_online_property Man page Source code
availability Man page Source code
barplot.mic Source code
barplot.rsi Source code
between Source code
brmo Man page Source code
bug_drug_combinations Man page Source code
c.ab Source code
c.disk Source code
c.mic Source code
c.mo Source code
c.rsi Source code
catalogue_of_life Man page
catalogue_of_life_version Man page Source code
check_dataset_integrity Source code
check_name Source code
class_integrity_check Source code
contains Source code
count Man page Source code
count_I Man page Source code
count_IR Man page Source code
count_R Man page Source code
count_S Man page Source code
count_SI Man page Source code
count_all Man page Source code
count_df Man page Source code
count_resistant Man page Source code
count_susceptible Man page Source code
create_MO.old_lookup Source code
create_MO_lookup Source code
dataset_UTF8_to_ASCII Source code
deparse1 Source code
desc Source code
disk Man page
distinct Source code
distinct.default Source code
distinct.grouped_data Source code
dots2vars Source code
droplevels.mic Source code
droplevels.rsi Source code
empty_result Source code
ends_with Source code
eucast_exceptional_phenotypes Man page Source code
eucast_rules Man page Source code
eval_call Source code
eval_expr Source code
everything Source code
example_isolates Man page
example_isolates_unclean Man page
exec_as.mo Source code
exec_as.rsi Source code
facet_rsi Man page Source code
filter Source code
filter.default Source code
filter.grouped_data Source code
filter_1st_cephalosporins Man page Source code
filter_2nd_cephalosporins Man page Source code
filter_3rd_cephalosporins Man page Source code
filter_4th_cephalosporins Man page Source code
filter_5th_cephalosporins Man page Source code
filter_ab_class Man page Source code
filter_aminoglycosides Man page Source code
filter_carbapenems Man page Source code
filter_cephalosporins Man page Source code
filter_first_isolate Man page Source code
filter_first_weighted_isolate Man page Source code
filter_fluoroquinolones Man page Source code
filter_glycopeptides Man page Source code
filter_join_worker Source code
filter_macrolides Man page Source code
filter_tetracyclines Man page Source code
find_ab_group Source code
find_ab_names Source code
first_isolate Man page Source code
font_black Source code
font_blue Source code
font_bold Source code
font_green Source code
font_green_bg Source code
font_grey Source code
font_italic Source code
font_magenta Source code
font_red Source code
font_red_bg Source code
font_silver Source code
font_stripstyle Source code
font_subtle Source code
font_underline Source code
font_white Source code
font_yellow Source code
font_yellow_bg Source code
format.bug_drug_combinations Man page Source code
format_uncertainty_as_df Source code
full_join Source code
full_join_microorganisms Man page Source code
g.test Man page Source code
generate_warning_abs_missing Source code
geom_rsi Man page Source code
get_column_abx Source code
get_groups Source code
get_guideline Source code
get_locale Man page Source code
get_mo_failures_uncertainties_renamed Source code
get_mo_source Man page Source code
ggplot_pca Man page Source code
ggplot_rsi Man page Source code
ggplot_rsi_predict Man page Source code
group_by Source code
guess_ab_col Man page Source code
has_colour Source code
has_groups Source code
if_else Source code
inner_join Man page Source code
inner_join_microorganisms Man page Source code
is.ab Man page Source code
is.disk Man page Source code
is.mic Man page Source code
is.mo Man page Source code
is.rsi Man page Source code
is.rsi.eligible Man page Source code
isFALSE Source code
join Man page
join_message Source code
join_worker Source code
joins_check_df Source code
key_antibiotics Man page Source code
key_antibiotics_equal Man page Source code
kurtosis Man page Source code
kurtosis.data.frame Man page Source code
kurtosis.default Man page Source code
kurtosis.matrix Man page Source code
labels_rsi_count Man page Source code
last_col Source code
left_join Source code
left_join_MO.old_lookup Source code
left_join_MO_lookup Source code
left_join_microorganisms Man page Source code
levenshtein_fraction Source code
lifecycle Man page
like Man page Source code
load_mo_failures_uncertainties_renamed Source code
make_trans_tbl Source code
matches Source code
mdr_cmi2012 Man page Source code
mdr_tb Man page Source code
mdro Man page Source code
mic Man page
microorganisms Man page
microorganisms.codes Man page
microorganisms.old Man page
mo Man page
mo_authors Man page Source code
mo_class Man page Source code
mo_failures Man page Source code
mo_family Man page Source code
mo_fullname Man page
mo_genus Man page Source code
mo_gramstain Man page Source code
mo_info Man page Source code
mo_kingdom Man page Source code
mo_name Man page Source code
mo_order Man page Source code
mo_phylum Man page Source code
mo_property Man page Source code
mo_rank Man page Source code
mo_ref Man page Source code
mo_renamed Man page Source code
mo_shortname Man page Source code
mo_snomed Man page Source code
mo_source Man page
mo_source_isvalid Source code
mo_species Man page Source code
mo_subspecies Man page Source code
mo_synonyms Man page Source code
mo_taxonomy Man page Source code
mo_type Man page Source code
mo_uncertainties Man page Source code
mo_url Man page Source code
mo_validate Source code
mo_year Man page Source code
mrgn Man page Source code
mutate Source code
mutate.default Source code
mutate.grouped_data Source code
n Source code
n_distinct Source code
n_rsi Man page
nr2char Source code
num_range Source code
p_symbol Man page Source code
parse_and_convert Source code
pca Man page Source code
pca_calculations Source code
peek_vars Source code
percentage Source code
plot.mic Source code
plot.resistance_predict Man page Source code
plot.rsi Source code
portion Man page
portion_I Man page Source code
portion_IR Man page Source code
portion_R Man page Source code
portion_S Man page Source code
portion_SI Man page Source code
portion_df Man page Source code
print.ab Source code
print.bug_drug_combinations Source code
print.catalogue_of_life_version Source code
print.disk Source code
print.grouped_data Source code
print.mic Source code
print.mo Source code
print.mo_renamed Source code
print.mo_uncertainties Source code
print.rsi Source code
progress_estimated Source code
proportion Man page
proportion_I Man page Source code
proportion_IR Man page Source code
proportion_R Man page Source code
proportion_S Man page Source code
proportion_SI Man page Source code
proportion_df Man page Source code
pull Source code
relocate Source code
rename Source code
resistance Man page Source code
resistance_predict Man page Source code
right_join Source code
right_join_microorganisms Man page Source code
round2 Source code
rownames_to_column Source code
rsi Man page
rsi_calc Source code
rsi_calc_df Source code
rsi_df Man page Source code
rsi_predict Man page
rsi_translation Man page
scale_rsi_colours Man page Source code
scale_y_percent Man page Source code
search_type_in_df Source code
select Source code
select_char Source code
select_positions Source code
select_symbol Source code
semi_join Source code
semi_join_microorganisms Man page Source code
set_groups Source code
set_mo_source Man page Source code
skewness Man page Source code
skewness.data.frame Man page Source code
skewness.default Man page Source code
skewness.matrix Man page Source code
split_into_groups Source code
starts_with Source code
stopifnot_installed_package Source code
stopifnot_msg Source code
strrep Source code
summary.mic Source code
summary.mo Source code
summary.rsi Source code
susceptibility Man page Source code
tally Source code
tally_n Source code
theme_rsi Man page Source code
to_class_mo Source code
translate Man page
translate_AMR Source code
translate_allow_uncertain Source code
trimws Source code
trimws2 Source code
try_colour Source code
ungroup Source code
unregex Source code
was_renamed Source code
AMR documentation built on July 8, 2020, 6:05 p.m.