P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-17 20:33:18 +02:00
Code Releases Activity

styled, unit test fix

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

74
man/as.rsi.Rd
View File

@ -164,27 +164,33 @@ example_isolates
summary(example_isolates) # see all R/SI results at a glance
# For INTERPRETING disk diffusion and MIC values -----------------------
# a whole data set, even with combined MIC values and disk zones
df <- data.frame(microorganism = "Escherichia coli",
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
NIT = as.mic(32),
ERY = "R")
df <- data.frame(
microorganism = "Escherichia coli",
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
NIT = as.mic(32),
ERY = "R"
)
as.rsi(df)
# for single values
as.rsi(x = as.mic(2),
mo = as.mo("S. pneumoniae"),
ab = "AMP",
guideline = "EUCAST")
as.rsi(
x = as.mic(2),
mo = as.mo("S. pneumoniae"),
ab = "AMP",
guideline = "EUCAST"
)
as.rsi(x = as.disk(18),
mo = "Strep pneu", # `mo` will be coerced with as.mo()
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST")
as.rsi(
x = as.disk(18),
mo = "Strep pneu", # `mo` will be coerced with as.mo()
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST"
)
\donttest{
# the dplyr way
@ -194,23 +200,27 @@ if (require("dplyr")) {
df \%>\% mutate(across(where(is.mic), as.rsi))
df \%>\% mutate_at(vars(AMP:TOB), as.rsi)
df \%>\% mutate(across(AMP:TOB, as.rsi))
df \%>\%
mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
# to include information about urinary tract infections (UTI)
data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
from_the_bladder = c(TRUE, FALSE)) \%>\%
data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
from_the_bladder = c(TRUE, FALSE)
) \%>\%
as.rsi(uti = "from_the_bladder")
data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")) \%>\%
data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")
) \%>\%
as.rsi() # automatically determines urine isolates
df \%>\%
mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
}
# For CLEANING existing R/SI values ------------------------------------
@ -219,22 +229,22 @@ as.rsi(c("S", "I", "R", "A", "B", "C"))
as.rsi("<= 0.002; S") # will return "S"
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
is.rsi(rsi_data)
plot(rsi_data) # for percentages
plot(rsi_data) # for percentages
barplot(rsi_data) # for frequencies
# the dplyr way
if (require("dplyr")) {
example_isolates \%>\%
mutate_at(vars(PEN:RIF), as.rsi)
# same:
# same:
example_isolates \%>\%
as.rsi(PEN:RIF)
# fastest way to transform all columns with already valid AMR results to class `rsi`:
example_isolates \%>\%
mutate_if(is.rsi.eligible, as.rsi)
# since dplyr 1.0.0, this can also be:
# since dplyr 1.0.0, this can also be:
# example_isolates \%>\%
# mutate(across(where(is.rsi.eligible), as.rsi))
}