P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 12:22:01 +02:00
Code Releases Activity

(v2.1.1.9054) fix examples

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-06-17 13:52:02 +02:00
parent 2dee1d71dc
commit 13baf8d7be
4 changed files with 156 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files

105
man/as.sir.Rd
View File

@ -256,32 +256,88 @@ summary(example_isolates) # see all SIR results at a glance
# For INTERPRETING disk diffusion and MIC values -----------------------
# example data sets, with combined MIC values and disk zones
df_wide <- data.frame(
microorganism = "Escherichia coli",
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
ERY = "R"
)
df_long <- data.frame(
bacteria = rep("Escherichia coli", 3),
antibiotic = c("amoxicillin", "cipro", "tobra", "genta"),
mics = as.mic(c(0.01, 1, 4, 8)),
disks = as.disk(c(6, 10, 14, 18))
)
\donttest{
## Using dplyr -------------------------------------------------
if (require("dplyr")) {
# approaches that all work without additional arguments:
df \%>\% mutate_if(is.mic, as.sir)
df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
df \%>\% mutate(across(where(is.mic), as.sir))
df \%>\% mutate_at(vars(AMP:TOB), as.sir)
df \%>\% mutate(across(AMP:TOB, as.sir))
df_wide \%>\% mutate_if(is.mic, as.sir)
df_wide \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
df_wide \%>\% mutate(across(where(is.mic), as.sir))
df_wide \%>\% mutate_at(vars(AMP:TOB), as.sir)
df_wide \%>\% mutate(across(AMP:TOB, as.sir))
# approaches that all work with additional arguments:
df \%>\% mutate_if(is.mic, as.sir, mo = "column1", guideline = "CLSI")
df \%>\% mutate(across(where(is.mic),
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
df \%>\% mutate_at(vars(AMP:TOB), as.sir, mo = "column1", guideline = "CLSI")
df \%>\% mutate(across(AMP:TOB,
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
df_long \%>\%
# given a certain data type, e.g. MIC values
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")
df_long \%>\%
mutate(across(where(is.mic),
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")))
df_long \%>\%
# given certain columns, e.g. from AMP to TOB
mutate_at(vars(AMP:TOB), as.sir,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")
df_long \%>\%
mutate(across(AMP:TOB,
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")))
# for veterinary breakpoints, add 'host':
df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "species_column")
df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "horse")
df \%>\% mutate(across(where(is.mic),
function(x) as.sir(x, guideline = "CLSI", host = "species_column")))
df \%>\% mutate_at(vars(AMP:TOB), as.sir, guideline = "CLSI", host = "species_column")
df \%>\% mutate(across(AMP:TOB,
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
df_long$animal_species <- c("cats", "dogs", "horses", "cattle")
df_long \%>\%
# given a certain data type, e.g. MIC values
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")
df_long \%>\%
mutate(across(where(is.mic),
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")))
df_long \%>\%
# given certain columns, e.g. from AMP to TOB
mutate_at(vars(AMP:TOB), as.sir,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")
df_long \%>\%
mutate(across(AMP:TOB,
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")))
# to include information about urinary tract infections (UTI)
data.frame(mo = "E. coli",
@ -294,23 +350,14 @@ if (require("dplyr")) {
specimen = c("urine", "blood")) \%>\%
as.sir() # automatically determines urine isolates
df \%>\%
df_wide \%>\%
mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
}
## Using base R ------------------------------------------------
# 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),
ERY = "R"
)
as.sir(df)
as.sir(df_wide)
# return a 'logbook' about the results:
sir_interpretation_history()