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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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36
man/count.Rd
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@ -129,9 +129,9 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
# run ?example_isolates for more info.
# base R ------------------------------------------------------------
count_resistant(example_isolates$AMX) # counts "R"
count_resistant(example_isolates$AMX) # counts "R"
count_susceptible(example_isolates$AMX) # counts "S" and "I"
count_all(example_isolates$AMX) # counts "S", "I" and "R"
count_all(example_isolates$AMX) # counts "S", "I" and "R"
# be more specific
count_S(example_isolates$AMX)
@ -156,36 +156,38 @@ susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
if (require("dplyr")) {
example_isolates \%>\%
group_by(ward) \%>\%
summarise(R = count_R(CIP),
I = count_I(CIP),
S = count_S(CIP),
n1 = count_all(CIP), # the actual total; sum of all three
n2 = n_rsi(CIP), # same - analogous to n_distinct
total = n()) # NOT the number of tested isolates!
summarise(
R = count_R(CIP),
I = count_I(CIP),
S = count_S(CIP),
n1 = count_all(CIP), # the actual total; sum of all three
n2 = n_rsi(CIP), # same - analogous to n_distinct
total = n()
) # NOT the number of tested isolates!
# Number of available isolates for a whole antibiotic class
# (i.e., in this data set columns GEN, TOB, AMK, KAN)
example_isolates \%>\%
group_by(ward) \%>\%
summarise(across(aminoglycosides(), n_rsi))
# Count co-resistance between amoxicillin/clav acid and gentamicin,
# so we can see that combination therapy does a lot more than mono therapy.
# Please mind that `susceptibility()` calculates percentages right away instead.
example_isolates \%>\% count_susceptible(AMC) # 1433
example_isolates \%>\% count_all(AMC) # 1879
example_isolates \%>\% count_all(AMC) # 1879
example_isolates \%>\% count_susceptible(GEN) # 1399
example_isolates \%>\% count_all(GEN) # 1855
example_isolates \%>\% count_all(GEN) # 1855
example_isolates \%>\% count_susceptible(AMC, GEN) # 1764
example_isolates \%>\% count_all(AMC, GEN) # 1936
example_isolates \%>\% count_all(AMC, GEN) # 1936
# Get number of S+I vs. R immediately of selected columns
example_isolates \%>\%
select(AMX, CIP) \%>\%
count_df(translate = FALSE)
# It also supports grouping variables
example_isolates \%>\%
select(ward, AMX, CIP) \%>\%